1
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Zhang H, Devoucoux M, Song X, Li L, Ayaz G, Cheng H, Tempel W, Dong C, Loppnau P, Côté J, Min J. Structural Basis for EPC1-Mediated Recruitment of MBTD1 into the NuA4/TIP60 Acetyltransferase Complex. Cell Rep 2021; 30:3996-4002.e4. [PMID: 32209463 DOI: 10.1016/j.celrep.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 01/01/2020] [Accepted: 02/28/2020] [Indexed: 12/28/2022] Open
Abstract
MBTD1, a H4K20me reader, has recently been identified as a component of the NuA4/TIP60 acetyltransferase complex, regulating gene expression and DNA repair. NuA4/TIP60 inhibits 53BP1 binding to chromatin through recognition of the H4K20me mark by MBTD1 and acetylation of H2AK15, blocking the ubiquitination mark required for 53BP1 localization at DNA breaks. The NuA4/TIP60 non-catalytic subunit EPC1 enlists MBTD1 into the complex, but the detailed molecular mechanism remains incompletely explored. Here, we present the crystal structure of the MBTD1-EPC1 complex, revealing a hydrophobic C-terminal fragment of EPC1 engaging the MBT repeats of MBTD1 in a site distinct from the H4K20me binding site. Different cellular assays validate the physiological significance of the key residues involved in the MBTD1-EPC1 interaction. Our study provides a structural framework for understanding the mechanism by which MBTD1 recruits the NuA4/TIP60 acetyltransferase complex to influence transcription and DNA repair pathway choice.
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Affiliation(s)
- Heng Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Maëva Devoucoux
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada
| | - Xiaosheng Song
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gamze Ayaz
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Biology, Middle East Technical University, Ankara, Turkey
| | - Harry Cheng
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jacques Côté
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology division of CHU de Québec-Université Laval Research Center, Quebec City, QC G1R 3S3, Canada.
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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2
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Schuhmacher MK, Beldar S, Khella MS, Bröhm A, Ludwig J, Tempel W, Weirich S, Min J, Jeltsch A. Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate. Commun Biol 2020; 3:511. [PMID: 32939018 PMCID: PMC7495481 DOI: 10.1038/s42003-020-01223-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
SETD2 catalyzes methylation at lysine 36 of histone H3 and it has many disease connections. We investigated the substrate sequence specificity of SETD2 and identified nine additional peptide and one protein (FBN1) substrates. Our data showed that SETD2 strongly prefers amino acids different from those in the H3K36 sequence at several positions of its specificity profile. Based on this, we designed an optimized super-substrate containing four amino acid exchanges and show by quantitative methylation assays with SETD2 that the super-substrate peptide is methylated about 290-fold more efficiently than the H3K36 peptide. Protein methylation studies confirmed very strong SETD2 methylation of the super-substrate in vitro and in cells. We solved the structure of SETD2 with bound super-substrate peptide containing a target lysine to methionine mutation, which revealed better interactions involving three of the substituted residues. Our data illustrate that substrate sequence design can strongly increase the activity of protein lysine methyltransferases. Schuhmacher, Beldar et al. design a super-substrate peptide based on the substrate sequence specificity of the SETD2 protein lysine methyltransferase. SETD2 methylates this super-substrate 290-fold more efficiently than the original H3K36 peptide. This study illustrates that substrate sequence design can improve the activity of protein lysine methyltransferases.
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Affiliation(s)
- Maren Kirstin Schuhmacher
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Serap Beldar
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Mina S Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.,Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jan Ludwig
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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3
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Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J. Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Cell Chem Biol 2020; 27:827-838.e7. [DOI: 10.1016/j.chembiol.2020.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
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4
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Mann MK, Franzoni I, de Freitas RF, Tempel W, Houliston S, Smith L, Vedadi M, Arrowsmith CH, Harding RJ, Schapira M. Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain. J Med Chem 2019; 62:10144-10155. [PMID: 31663737 DOI: 10.1021/acs.jmedchem.9b00988] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship, which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signaling pathways in health and disease.
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Affiliation(s)
- Mandeep K Mann
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Ivan Franzoni
- Department of Chemistry , University of Toronto , 80 St. George St. , Toronto , Ontario M5S 3H6 , Canada
| | - Renato Ferreira de Freitas
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada
| | - Scott Houliston
- University Health Network , 661 University Avenue , Toronto , Ontario M5G 2C4 , Canada
| | - Leanna Smith
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada.,University Health Network , 661 University Avenue , Toronto , Ontario M5G 2C4 , Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre , South Tower, 101 College St., Suite 700 , Toronto , Ontario M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
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5
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Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M. The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 2019; 8:45403. [PMID: 31081496 PMCID: PMC6579520 DOI: 10.7554/elife.45403] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/08/2019] [Indexed: 12/27/2022] Open
Abstract
Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illuminate the conformational landscapes of target proteins. SETD8 is a protein lysine methyltransferase (PKMT), which functions in vivo via the methylation of histone and nonhistone targets. Utilizing covalent inhibitors and depleting native ligands to trap hidden conformational states, we obtained diverse X-ray structures of SETD8. These structures were used to seed distributed atomistic molecular dynamics simulations that generated a total of six milliseconds of trajectory data. Markov state models, built via an automated machine learning approach and corroborated experimentally, reveal how slow conformational motions and conformational states are relevant to catalysis. These findings provide molecular insight on enzymatic catalysis and allosteric mechanisms of a PKMT via its detailed conformational landscape. Our cells contain thousands of proteins that perform many different tasks. Such tasks often involve significant changes in the shape of a protein that allow it to interact with other proteins or ligands. Understanding these shape changes can be an essential step for predicting and manipulating how proteins work or designing new drugs. Some changes in protein shape happen quickly, whereas others take longer. Existing experimental approaches generally only capture some, but not all, of the different shapes an individual protein adopts. A family of proteins known as protein lysine methyltransferases (PKMTs) help to regulate the activities of other proteins by adding small tags called methyl groups to specific positions on their target proteins. PKMTs play important roles in many life processes including in activating genes, maintaining stem cells and controlling how organs develop. It is important for cells to properly control the activity of PKMTs because too much, or too little, activity can promote cancers and neurological diseases. For example, genetic mutations that increase the levels of a PKMT known as SETD8 appear to promote the progression of some breast cancers and childhood leukemia. There is a pressing need to develop new drugs that can inhibit SETD8 and other PKMTs in human patients. However, these efforts are hindered by the lack of understanding of exactly how the shape of PKMT proteins change as they operate in cells. Chen, Wiewiora et al. used a technique called X-ray crystallography to generate structural models of the human SETD8 protein in the presence or absence of native or foreign ligands. These models were used to develop computer simulations of how the shape of SETD8 changes as it operates. Further computational analysis and laboratory experiments revealed how slow changes in the shape of SETD8 contribute to the ability of the protein to attach methyl groups to other proteins. This work is a significant stepping-stone to developing a complete model of how the SETD8 protein works, as well as understanding how genetic mutations may affect the protein’s role in the body. The next step is to refine the model by integrating data from other approaches including biophysical models and mathematical calculations of the energy associated with the shape changes, with a long-term goal to better understand and then manipulate the function of SETD8.
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Affiliation(s)
- Shi Chen
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, United States.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Rafal P Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, United States.,Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Fanwang Meng
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Nicolas Babault
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Anqi Ma
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Kun Qian
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Hua Zou
- Takeda California, Science Center Drive, San Diego, United States
| | - Junyi Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shijie Fan
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gil Blum
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Fabio Pittella-Silva
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kyle A Beauchamp
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Hualiang Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaixian Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Robert J Skene
- Takeda California, Science Center Drive, San Diego, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, United States
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6
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Walker BC, Tempel W, Zhu H, Park H, Cochran JC. Chromokinesins NOD and KID Use Distinct ATPase Mechanisms and Microtubule Interactions To Perform a Similar Function. Biochemistry 2019; 58:2326-2338. [PMID: 30973712 DOI: 10.1021/acs.biochem.9b00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromokinesins NOD and KID have similar DNA binding domains and functions during cell division, while their motor domain sequences show significant variations. It has been unclear whether these motors have the similar structure, chemistry, and microtubule interactions necessary to follow a similar mechanism of force generation. We used biochemical rate measurements, cosedimentation, and structural analysis to investigate the ATPase mechanisms of the NOD and KID core domains. These studies revealed that NOD and KID have different ATPase mechanisms, microtubule interactions, and catalytic domain structures. The ATPase cycles of NOD and KID have different rate-limiting steps. The ATPase rate of NOD was robustly stimulated by microtubules, and its microtubule affinity was weakened in all nucleotide-bound states. KID bound microtubules tightly in all nucleotide states and remained associated with the microtubule for more than 100 cycles of ATP hydrolysis before dissociating. The structure of KID was most like that of conventional kinesin (KIF5). Key differences in the microtubule binding region and allosteric communication pathway between KID and NOD are consistent with our biochemical data. Our results support the model in which NOD and KID utilize distinct mechanistic pathways to achieve the same function during cell division.
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Affiliation(s)
- Benjamin C Walker
- Department of Molecular & Cellular Biochemistry , Indiana University , Simon Hall Room 405C, 212 South Hawthorne Drive , Bloomington , Indiana 47405 , United States
| | - Wolfram Tempel
- Structural Genomics Consortium , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Haizhong Zhu
- Structural Genomics Consortium , University of Toronto , Toronto , Ontario M5G 1L7 , Canada
| | - Heewon Park
- Department of Biochemistry and Molecular Biology , Tulane School of Medicine , New Orleans , Louisiana 70112 , United States
| | - Jared C Cochran
- Department of Molecular & Cellular Biochemistry , Indiana University , Simon Hall Room 405C, 212 South Hawthorne Drive , Bloomington , Indiana 47405 , United States
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7
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Dong C, Dong G, Li L, Zhu L, Tempel W, Liu Y, Huang R, Min J. An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2. Commun Biol 2018; 1:183. [PMID: 30417120 PMCID: PMC6214909 DOI: 10.1038/s42003-018-0196-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/15/2018] [Indexed: 01/11/2023] Open
Abstract
α-N-terminal methylation of proteins is an important post-translational modification that is catalyzed by two different N-terminal methyltransferases, namely NTMT1 and NTMT2. Previous studies have suggested that NTMT1 is a tri-methyltransferase, whereas NTMT2 is a mono-methyltransferase. Here, we report the first crystal structures, to our knowledge, of NTMT2 in binary complex with S-adenosyl-L-methionine as well as in ternary complex with S-adenosyl-L-homocysteine and a substrate peptide. Our structural observations combined with biochemical studies reveal that NTMT2 is also able to di-/tri-methylate the GPKRIA peptide and di-methylate the PPKRIA peptide, otherwise it is predominantly a mono-methyltransferase. The residue N89 of NTMT2 serves as a gatekeeper residue that regulates the binding of unmethylated versus monomethylated substrate peptide. Structural comparison of NTMT1 and NTMT2 prompts us to design a N89G mutant of NTMT2 that can profoundly alter its catalytic activities and product specificities. Cheng Dong et al. resolve the crystal structure of NTMT2, presenting the molecular basis for substrate recognition. Using structural and biochemical studies, they identified a specific residue within NTMT2 that controls its binding affinity to unmethylated or monomethylated substrates.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Licheng Zhu
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada.,School of Life Sciences, Jinggangshan University, 343009, Ji'an, Jiangxi, China
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA.
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, M5G1L7, ON, Canada. .,Department of Physiology, University of Toronto, Toronto, M5S 1A8, ON, Canada.
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8
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Madigan JP, Hou F, Ye L, Hu J, Dong A, Tempel W, Yohe ME, Randazzo PA, Jenkins LMM, Gottesman MM, Tong Y. The tuberous sclerosis complex subunit TBC1D7 is stabilized by Akt phosphorylation-mediated 14-3-3 binding. J Biol Chem 2018; 293:16142-16159. [PMID: 30143532 DOI: 10.1074/jbc.ra118.003525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/13/2018] [Indexed: 01/19/2023] Open
Abstract
The tuberous sclerosis complex (TSC) is a negative regulator of mTOR complex 1, a signaling node promoting cellular growth in response to various nutrients and growth factors. However, several regulators in TSC signaling still await discovery and characterization. Using pulldown and MS approaches, here we identified the TSC complex member, TBC1 domain family member 7 (TBC1D7), as a binding partner for PH domain and leucine-rich repeat protein phosphatase 1 (PHLPP1), a negative regulator of Akt kinase signaling. Most TBC domain-containing proteins function as Rab GTPase-activating proteins (RabGAPs), but the crystal structure of TBC1D7 revealed that it lacks residues critical for RabGAP activity. Sequence analysis identified a putative site for both Akt-mediated phosphorylation and 14-3-3 binding at Ser-124, and we found that Akt phosphorylates TBC1D7 at Ser-124. However, this phosphorylation had no effect on the binding of TBC1D7 to TSC1, but stabilized TBC1D7. Moreover, 14-3-3 protein both bound and stabilized TBC1D7 in a growth factor-dependent manner, and a phospho-deficient substitution, S124A, prevented this interaction. The crystal structure of 14-3-3ζ in complex with a phospho-Ser-124 TBC1D7 peptide confirmed the direct interaction between 14-3-3 and TBC1D7. The sequence immediately upstream of Ser-124 aligned with a canonical β-TrCP degron, and we found that the E3 ubiquitin ligase β-TrCP2 ubiquitinates TBC1D7 and decreases its stability. Our findings reveal that Akt activity determines the phosphorylation status of TBC1D7 at the phospho-switch Ser-124, which governs binding to either 14-3-3 or β-TrCP2, resulting in increased or decreased stability of TBC1D7, respectively.
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Affiliation(s)
| | - Feng Hou
- the Structural Genomics Consortium and
| | - Linlei Ye
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada, and
| | | | | | | | | | - Paul A Randazzo
- Laboratory of Cell and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | | | | | - Yufeng Tong
- the Structural Genomics Consortium and .,the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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9
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Zhang H, Zhou B, Qin S, Xu J, Harding R, Tempel W, Nayak V, Li Y, Loppnau P, Dou Y, Min J. Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis. Genes Dev 2018; 32:341-346. [PMID: 29563185 PMCID: PMC5900708 DOI: 10.1101/gad.311639.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/01/2018] [Indexed: 11/24/2022]
Abstract
The mixed-lineage leukemia (MLL)-AF10 fusion oncoprotein recruits DOT1L to the homeobox A (HOXA) gene cluster through its octapeptide motif leucine zipper (OM-LZ), thereby inducing and maintaining the MLL-AF10-associated leukemogenesis. However, the recognition mechanism between DOT1L and MLL-AF10 is unclear. Here, we present the crystal structures of both apo AF10OM-LZ and its complex with the coiled-coil domain of DOT1L. Disruption of the DOT1L-AF10 interface abrogates MLL-AF10-associated leukemic transformation. We further show that zinc stabilizes the DOT1L-AF10 complex and may be involved in the regulation of the HOXA gene expression. Our studies may also pave the way for the rational design of therapeutic drugs against MLL-rearranged leukemia.
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Affiliation(s)
- Heng Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Life Science Research Center, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rachel Harding
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Vinod Nayak
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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10
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Jurkowska RZ, Qin S, Kungulovski G, Tempel W, Liu Y, Bashtrykov P, Stiefelmaier J, Jurkowski TP, Kudithipudi S, Weirich S, Tamas R, Wu H, Dombrovski L, Loppnau P, Reinhardt R, Min J, Jeltsch A. H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat Commun 2017; 8:2057. [PMID: 29234025 PMCID: PMC5727127 DOI: 10.1038/s41467-017-02259-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.
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Affiliation(s)
- Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Life Science Research Center, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Judith Stiefelmaier
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Srikanth Kudithipudi
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Raluca Tamas
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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11
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Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J. Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. J Biol Chem 2017; 292:5655-5664. [PMID: 28223359 DOI: 10.1074/jbc.m116.768374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/16/2017] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. We consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Ming Lei
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yuzhe Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yanjun Li
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and .,the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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12
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Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure 2016; 24:502-508. [PMID: 27050687 DOI: 10.1016/j.str.2016.02.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
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Affiliation(s)
- Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley Laboratory, Department of Bioengineering, UC Berkeley, Berkeley, CA 94720-8235, USA
| | | | - Cary Bauer
- Bruker AXS, Inc., Madison, WI 53711, USA
| | | | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Talapady N Bhat
- Biosystems and Biomaterials Division, NIST, Gaithersburg, MD 20899, USA
| | | | - Evan Bolton
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | | | - David Brown
- School of Biosciences, University of Kent, Canterbury CT2 7NH, UK; Charles River Ltd., Structural Biology and Biophysics, Cambridge CB10 1XL, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kirk L Clark
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Tom Darden
- OpenEye Scientific, Cambridge, MA 02142, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Victoria A Feher
- Drug Design Data Resource and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Colin R Groom
- Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK.
| | | | - Jorg Hendle
- Structural Biology, Lilly Biotechnology Center, San Diego, CA 92121, USA
| | | | - Andrzej Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Joseph Marcotrigiano
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - John L Markley
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Matthew Miller
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Atsushi Nakagawa
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - Marc Nicklaus
- Computer-Aided Drug Design Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | | | | | | | - Susan Pieniazek
- Bristol-Myers Squibb Research and Development, Pennington, NJ 08534, USA
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steven Sheriff
- Bristol-Myers Squibb Research and Development, Princeton, NJ 08543, USA
| | - Oliver Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - John Spurlino
- Janssen Pharmaceuticals, Inc., Spring House, PA 19002, USA
| | - Terry Stouch
- Science For Solutions, LLC, West Windsor, NJ 08550, USA
| | - Radka Svobodova
- CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Brno, 625 00 Brno, Czech Republic
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | - Dale Tronrud
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suzanna C Ward
- Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK
| | | | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Huanwang Yang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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13
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Butler KV, Ma A, Yu W, Li F, Tempel W, Babault N, Pittella-Silva F, Shao J, Wang J, Luo M, Vedadi M, Brown PJ, Arrowsmith CH, Jin J. Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. J Med Chem 2016; 59:9881-9889. [PMID: 27804297 DOI: 10.1021/acs.jmedchem.6b01244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective inhibitors of protein lysine methyltransferases, including SET domain-containing protein 8 (SETD8), are highly desired, as only a fraction of these enzymes are associated with high-quality inhibitors. From our previously discovered SETD8 inhibitor, we developed a more potent analog and solved a cocrystal structure, which is the first crystal structure of SETD8 in complex with a small-molecule inhibitor. This cocrystal structure allowed the design of a covalent inhibitor of SETD8 (MS453), which specifically modifies a cysteine residue near the inhibitor binding site, has an IC50 value of 804 nM, reacts with SETD8 with near-quantitative yield, and is selective for SETD8 against 28 other methyltransferases. We also solved the crystal structure of the covalent inhibitor in complex with SETD8. This work provides atomic-level perspective on the inhibition of SETD8 by small molecules and will help identify high-quality chemical probes of SETD8.
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Affiliation(s)
- Kyle V Butler
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Anqi Ma
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Nicolas Babault
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Fabio Pittella-Silva
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Jason Shao
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Junyi Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Jian Jin
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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14
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Hughes SJ, Barnard L, Mottaghi K, Tempel W, Antoshchenko T, Hong BS, Allali-Hassani A, Smil D, Vedadi M, Strauss E, Park HW. Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product. ACS Infect Dis 2016; 2:627-641. [PMID: 27759386 DOI: 10.1021/acsinfecdis.6b00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanKII), the first enzyme of coenzyme A biosynthesis. This mechanism of action follows from SaPanKII having a binding mode for PanAms that is distinct from those of other PanKs. To dissect the molecular interactions responsible for PanAm inhibitory activity, we conducted a mini SAR study in tandem with the cocrystallization of SaPanKII with two classic PanAms (N5-Pan and N7-Pan), culminating in the synthesis and characterization of two new PanAms, N-Pip-PanAm and MeO-N5-PanAm. The cocrystal structures showed that all of the PanAms are phosphorylated by SaPanKII but remain bound at the active site; this occurs primarily through interactions with Tyr240' and Thr172'. Kinetic analysis showed a strong correlation between kcat (slow PanAm turnover) and IC50 (inhibition of pantothenate phosphorylation) values, suggesting that SaPanKII inhibition occurs via a delay in product release. In-depth analysis of the PanAm-bound structures showed that the capacity for accepting a hydrogen bond from the amide of Thr172' was a stronger determinant for PanAm potency than the capacity to π-stack with Tyr240'. The two new PanAms, N-Pip-PanAm and MeO-N5-PanAm, effectively combine both hydrogen bonding and hydrophobic interactions, resulting in the most potent SaPanKII inhibition described to date. Taken together, our results are consistent with an inhibition mechanism wherein PanAms act as SaPanKII substrates that remain bound upon phosphorylation. The phospho-PanAm-SaPanKII interactions described herein may help future antistaphylococcal drug development.
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Affiliation(s)
| | - Leanne Barnard
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | | | | | - Tetyana Antoshchenko
- Department
of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112, United States
| | | | | | | | | | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hee-Won Park
- Department
of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112, United States
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15
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Spurr SS, Bayle ED, Yu W, Li F, Tempel W, Vedadi M, Schapira M, Fish PV. New small molecule inhibitors of histone methyl transferase DOT1L with a nitrile as a non-traditional replacement for heavy halogen atoms. Bioorg Med Chem Lett 2016; 26:4518-4522. [DOI: 10.1016/j.bmcl.2016.07.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/16/2022]
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16
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Li W, Zhao A, Tempel W, Loppnau P, Liu Y. Crystal structure of DPF3b in complex with an acetylated histone peptide. J Struct Biol 2016; 195:365-372. [PMID: 27402533 DOI: 10.1016/j.jsb.2016.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 12/15/2022]
Abstract
Histone acetylation plays an important role in chromatin dynamics and is associated with active gene transcription. This modification is written by acetyltransferases, erased by histone deacetylases and read out by bromodomain containing proteins, and others such as tandem PHD fingers of DPF3b. Here we report the high resolution crystal structure of the tandem PHD fingers of DPF3b in complex with an H3K14ac peptide. In the complex structure, the histone peptide adopts an α-helical conformation, unlike previously observed by NMR, but similar to a previously reported MOZ-H3K14ac complex structure. Our crystal structure adds to existing evidence that points to the α-helix as a natural conformation of histone tails as they interact with histone-associated proteins.
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Affiliation(s)
- Weiguo Li
- Key Laboratory of Pesticide & Chemical Biology, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Anthony Zhao
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China.
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17
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Liu S, Wu X, Zong M, Tempel W, Loppnau P, Liu Y. Structural basis for a novel interaction between TXNIP and Vav2. FEBS Lett 2016; 590:857-65. [DOI: 10.1002/1873-3468.12110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/08/2016] [Accepted: 02/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shasha Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Xue Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Minru Zong
- China-Japan Union Hospital of Jilin University; Changchun China
| | - Wolfram Tempel
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Peter Loppnau
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
- Structural Genomics Consortium; University of Toronto; Ontario Canada
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18
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Liu Y, Tempel W, Zhang Q, Liang X, Loppnau P, Qin S, Min J. Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins. J Biol Chem 2016; 291:9000-13. [PMID: 26933034 DOI: 10.1074/jbc.m116.718973] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/08/2023] Open
Abstract
Covalent modifications of histone N-terminal tails play a critical role in regulating chromatin structure and controlling gene expression. These modifications are controlled by histone-modifying enzymes and read out by histone-binding proteins. Numerous proteins have been identified as histone modification readers. Here we report the family-wide characterization of histone binding abilities of human CW domain-containing proteins. We demonstrate that the CW domains in ZCWPW2 and MORC3/4 selectively recognize histone H3 trimethylated at Lys-4, similar to ZCWPW1 reported previously, while the MORC1/2 and LSD2 lack histone H3 Lys-4 binding ability. Our crystal structures of the CW domains of ZCWPW2 and MORC3 in complex with the histone H3 trimethylated at Lys-4 peptide reveal the molecular basis of this interaction. In each complex, two tryptophan residues in the CW domain form the "floor" and "right wall," respectively, of the methyllysine recognition cage. Our mutation results based on ZCWPW2 reveal that the right wall tryptophan residue is essential for binding, and the floor tryptophan residue enhances binding affinity. Our structural and mutational analysis highlights the conserved roles of the cage residues of CW domain across the histone methyllysine binders but also suggests why some CW domains lack histone binding ability.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Qi Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Xiao Liang
- the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Life Science Research Center, South University of Science and Technology of China, Shenzhen 518055, China, and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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19
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Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV. A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Nat Chem Biol 2016; 12:180-7. [PMID: 26807715 PMCID: PMC4755828 DOI: 10.1038/nchembio.2007] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022]
Abstract
We report the design and characterization of UNC3866, a potent antagonist of the methyl-lysine (Kme) reading function of the Polycomb CBX and CDY families of chromodomains. Polycomb CBX proteins regulate gene expression by targeting Polycomb Repressive Complex 1 to sites of H3K27me3 via their chromodomains. UNC3866 binds the chromodomains of CBX4 and CBX7 most potently with a Kd of ∼100 nM for each, and is 6- to 18-fold selective versus seven other CBX and CDY chromodomains while being highly selective versus >250 other protein targets. X-ray crystallography revealed that UNC3866 closely mimics the interactions of the methylated H3 tail with these chromodomains. UNC4195, a biotinylated derivative of UNC3866, was used to demonstrate that UNC3866 engages intact PRC1 and that EED incorporation into PRC1 is isoform-dependent in PC3 prostate cancer cells. Finally, UNC3866 inhibits PC3 cell proliferation, a known CBX7 phenotype, while UNC4219, a methylated negative control compound, has negligible effects.
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Affiliation(s)
- Jacob I Stuckey
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradley M Dickson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy Cheng
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Jacqueline L Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie H Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Katherine G Huber
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Karynne Black
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Xi-Ping Huang
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill Medical School, Chapel Hill, North Carolina, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill Medical School, Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill Medical School, Chapel Hill, North Carolina, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill Medical School, Chapel Hill, North Carolina, USA
| | - Brandi M Baughman
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Samantha G Pattenden
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Xu C, Wang X, Liu K, Roundtree IA, Tempel W, Li Y, Lu Z, He C, Min J. Corrigendum: Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain. Nat Chem Biol 2015; 11:815. [PMID: 26379027 DOI: 10.1038/nchembio1015-815c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Dong C, Mao Y, Tempel W, Qin S, Li L, Loppnau P, Huang R, Min J. Structural basis for substrate recognition by the human N-terminal methyltransferase 1. Genes Dev 2015; 29:2343-8. [PMID: 26543161 PMCID: PMC4691889 DOI: 10.1101/gad.270611.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/14/2015] [Indexed: 01/17/2023]
Abstract
α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological substrates propels the elucidation of a general role of α-N-terminal methylation in mediating DNA-binding ability of the modified proteins. The phenotypes, observed from both NTMT1 knockdown in breast cancer cell lines and knockout mouse models, suggest the potential involvement of α-N-terminal methylation in DNA damage response and cancer development. In this study, we report the first crystal structures of human NTMT1 in complex with cofactor S-adenosyl-L-homocysteine (SAH) and six substrate peptides, respectively, and reveal that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity. Our complex structures, coupled with mutagenesis, binding, and enzymatic studies, also present the key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for α-N-terminal methylation and explain why NTMT1 prefers an XPK sequence motif. We propose a catalytic mechanism for α-N-terminal methylation. Overall, this study gives us the first glimpse of the molecular mechanism of α-N-terminal methylation and potentially contributes to the advent of therapeutic agents for human diseases associated with deregulated α-N-terminal methylation.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Yunfei Mao
- Department of Medicinal Chemistry, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA; The Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada
| | - Rong Huang
- Department of Medicinal Chemistry, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA; The Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontaria M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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22
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Wu H, Zeng H, Lam R, Tempel W, Kerr ID, Min J. Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome. Acta Crystallogr F Struct Biol Commun 2015; 71:981-5. [PMID: 26249686 PMCID: PMC4528928 DOI: 10.1107/s2053230x15010183] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/26/2015] [Indexed: 02/25/2023] Open
Abstract
Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson-Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.
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Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Iain D. Kerr
- Myriad Genetic Laboratories Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5G 1L7, Canada
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23
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Nie J, Xu C, Jin J, Aka JA, Tempel W, Nguyen V, You L, Weist R, Min J, Pawson T, Yang XJ. Ankyrin repeats of ANKRA2 recognize a PxLPxL motif on the 3M syndrome protein CCDC8. Structure 2015; 23:700-12. [PMID: 25752541 DOI: 10.1016/j.str.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
Abstract
Peptide motifs are often used for protein-protein interactions. We have recently demonstrated that ankyrin repeats of ANKRA2 and the paralogous bare lymphocyte syndrome transcription factor RFXANK recognize PxLPxL/I motifs shared by megalin, three histone deacetylases, and RFX5. We show here that that CCDC8 is a major partner of ANKRA2 but not RFXANK in cells. The CCDC8 gene is mutated in 3M syndrome, a short-stature disorder with additional facial and skeletal abnormalities. Two other genes mutated in this syndrome encode CUL7 and OBSL1. While CUL7 is a ubiquitin ligase and OBSL1 associates with the cytoskeleton, little is known about CCDC8. Binding and structural analyses reveal that the ankyrin repeats of ANKRA2 recognize a PxLPxL motif at the C-terminal region of CCDC8. The N-terminal part interacts with OBSL1 to form a CUL7 ligase complex. These results link ANKRA2 unexpectedly to 3M syndrome and suggest novel regulatory mechanisms for histone deacetylases and RFX7.
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Affiliation(s)
- Jianyun Nie
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada; Department of Breast Cancer, The Third Affiliated Hospital, Kunming Medical University, Yunnan 650118, China
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Jing Jin
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Juliette A Aka
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Vivian Nguyen
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Linya You
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Ryan Weist
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Tony Pawson
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada; McGill University Health Center, Montréal, QC H3A 1A3, Canada.
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24
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Qin S, Liu Y, Tempel W, Eram M, Bian C, Liu K, Senisterra G, Crombet L, Vedadi M. Histone mimicry and hijacking of host proteins by influenza virus protein NS1. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314084083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Pathogens can interfere with vital biological processes of their host by mimicking host proteins. The NS1 protein of the influenza A H3N2 subtype possesses a histone H3K4-like sequence at its carboxyl terminus and has been reported to use this mimic to hijack host proteins. However, this mimic lacks a free N-terminus that is essential for binding to many known H3K4 readers. Here we show that the double chromodomains of CHD1adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. We also explored the possibility that NS1 hijacks other cellular proteins and found that the NS1 mimic has access to only a subset of chromatin-associated factors, such as WDR5. Moreover, methylation of the NS1 mimic can not be reversed by the H3K4 demethylase LSD1. Overall, we thus conclude that the NS1 mimic is an imperfect histone mimic.
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25
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Tempel W, Grabovec I, MacKenzie F, Dichenko YV, Usanov SA, Gilep AA, Park HW, Strushkevich N. Structural characterization of human cholesterol 7α-hydroxylase. J Lipid Res 2014; 55:1925-32. [PMID: 24927729 DOI: 10.1194/jlr.m050765] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Hepatic conversion to bile acids is a major elimination route for cholesterol in mammals. CYP7A1 catalyzes the first and rate-limiting step in classic bile acid biosynthesis, converting cholesterol to 7α-hydroxycholesterol. To identify the structural determinants that govern the stereospecific hydroxylation of cholesterol, we solved the crystal structure of CYP7A1 in the ligand-free state. The structure-based mutation T104L in the B' helix, corresponding to the nonpolar residue of CYP7B1, was used to obtain crystals of complexes with cholest-4-en-3-one and with cholesterol oxidation product 7-ketocholesterol (7KCh). The structures reveal a motif of residues that promote cholest-4-en-3-one binding parallel to the heme, thus positioning the C7 atom for hydroxylation. Additional regions of the binding cavity (most distant from the access channel) are involved to accommodate the elongated conformation of the aliphatic side chain. Structural complex with 7KCh shows an active site rigidity and provides an explanation for its inhibitory effect. Based on our previously published data, we proposed a model of cholesterol abstraction from the membrane by CYP7A1 for metabolism. CYP7A1 structural data provide a molecular basis for understanding of the diversity of 7α-hydroxylases, on the one hand, and cholesterol-metabolizing enzymes adapted for their specific activity, on the other hand.
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Affiliation(s)
- Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Irina Grabovec
- Institute of Bioorganic Chemistry NAS of Belarus, Minsk, 220141 Belarus
| | - Farrell MacKenzie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | | | - Sergey A Usanov
- Institute of Bioorganic Chemistry NAS of Belarus, Minsk, 220141 Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry NAS of Belarus, Minsk, 220141 Belarus
| | - Hee-Won Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
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Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J Biol Chem 2014; 289:17299-311. [PMID: 24778178 DOI: 10.1074/jbc.m114.550350] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N(6)-Methyladenosine (m(6)A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m(6)A in single-stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both single-stranded RNA and single-stranded DNA. We identify the TCA cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50, ∼488 μm). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond that apparently excludes the binding of dsDNA to ALKBH5. We identify the m(6)A binding pocket of ALKBH5 and the key residues involved in m(6)A recognition using mutagenesis and ITC binding experiments.
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Affiliation(s)
- Chao Xu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Wolfram Tempel
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Marina Demetriades
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - WeiShen Aik
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Christopher J Schofield
- the Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom, and
| | - Jinrong Min
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, From the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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27
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Li B, Tempel W, Smil D, Bolshan Y, Schapira M, Park HW. Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides. Proteins 2013; 81:1466-72. [PMID: 23553820 DOI: 10.1002/prot.24290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 03/05/2013] [Accepted: 03/07/2013] [Indexed: 11/12/2022]
Abstract
N-Substituted pantothenamides are derivatives of pantothenate, the precursor in the biosynthesis of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis and possess antimicrobial activity against various pathogenic bacteria. Here we solved the crystal structure of the Klebsiella pneumoniae PanK (KpPanK) in complex with N-pentylpantothenamide (N5-Pan) to understand the molecular basis of its antimicrobial activity. The structure reveals a polar pocket interacting with the pantothenate moiety of N5-Pan and an aromatic pocket loosely protecting the pentyl tail, suggesting that the introduction of an aromatic ring to a new pantothenamide may enhance the compound's affinity to KpPanK. To test this idea, we synthesized N-pyridin-3-ylmethylpantothenamide (Np-Pan) and solved its co-crystal structure with KpPanK. The structure reveals two alternat conformations of the aromatic ring of Np-Pan bound at the aromatic pocket, providing the basis for further improvement of pantothenamide binding to KpPanK.
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Affiliation(s)
- Buren Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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28
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Yu W, Chory EJ, Wernimont AK, Tempel W, Scopton A, Federation A, Marineau JJ, Qi J, Barsyte-Lovejoy D, Yi J, Marcellus R, Iacob RE, Engen JR, Griffin C, Aman A, Wienholds E, Li F, Pineda J, Estiu G, Shatseva T, Hajian T, Al-Awar R, Dick JE, Vedadi M, Brown PJ, Arrowsmith CH, Bradner JE, Schapira M. Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors. Nat Commun 2013; 3:1288. [PMID: 23250418 DOI: 10.1038/ncomms2304] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/15/2012] [Indexed: 01/04/2023] Open
Abstract
Selective inhibition of protein methyltransferases is a promising new approach to drug discovery. An attractive strategy towards this goal is the development of compounds that selectively inhibit binding of the cofactor, S-adenosylmethionine, within specific protein methyltransferases. Here we report the three-dimensional structure of the protein methyltransferase DOT1L bound to EPZ004777, the first S-adenosylmethionine-competitive inhibitor of a protein methyltransferase with in vivo efficacy. This structure and those of four new analogues reveal remodelling of the catalytic site. EPZ004777 and a brominated analogue, SGC0946, inhibit DOT1L in vitro and selectively kill mixed lineage leukaemia cells, in which DOT1L is aberrantly localized via interaction with an oncogenic MLL fusion protein. These data provide important new insight into mechanisms of cell-active S-adenosylmethionine-competitive protein methyltransferase inhibitors, and establish a foundation for the further development of drug-like inhibitors of DOT1L for cancer therapy.
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Affiliation(s)
- Wenyu Yu
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
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Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJC, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell 2013; 151:1200-13. [PMID: 23217707 DOI: 10.1016/j.cell.2012.11.014] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/19/2012] [Accepted: 11/09/2012] [Indexed: 11/26/2022]
Abstract
Ten-Eleven Translocation (Tet) family of dioxygenases dynamically regulates DNA methylation and has been implicated in cell lineage differentiation and oncogenesis. Yet their functions and mechanisms of action in gene regulation and embryonic development are largely unknown. Here, we report that Xenopus Tet3 plays an essential role in early eye and neural development by directly regulating a set of key developmental genes. Tet3 is an active 5mC hydroxylase regulating the 5mC/5hmC status at target gene promoters. Biochemical and structural studies further demonstrate that the Tet3 CXXC domain is critical for specific Tet3 targeting. Finally, we show that the enzymatic activity and CXXC domain are both crucial for Tet3's biological function. Together, these findings define Tet3 as a transcription regulator and reveal a molecular mechanism by which the 5mC hydroxylase and DNA binding activities of Tet3 cooperate to control target gene expression and embryonic development.
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Affiliation(s)
- Yufei Xu
- Division of Endocrinology, Diabetes and Hypertension, Departments of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Yu W, Smil D, Li F, Tempel W, Fedorov O, Nguyen KT, Bolshan Y, Al-Awar R, Knapp S, Arrowsmith CH, Vedadi M, Brown PJ, Schapira M. Bromo-deaza-SAH: a potent and selective DOT1L inhibitor. Bioorg Med Chem 2013; 21:1787-1794. [PMID: 23433670 DOI: 10.1016/j.bmc.2013.01.049] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/11/2013] [Accepted: 01/20/2013] [Indexed: 12/23/2022]
Abstract
Chemical inhibition of proteins involved in chromatin-mediated signaling is an emerging strategy to control chromatin compaction with the aim to reprogram expression networks to alter disease states. Protein methyltransferases constitute one of the protein families that participate in epigenetic control of gene expression, and represent a novel therapeutic target class. Recruitment of the protein lysine methyltransferase DOT1L at aberrant loci is a frequent mechanism driving acute lymphoid and myeloid leukemias, particularly in infants, and pharmacological inhibition of DOT1L extends survival in a mouse model of mixed lineage leukemia. A better understanding of the structural chemistry of DOT1L inhibition would accelerate the development of improved compounds. Here, we report that the addition of a single halogen atom at a critical position in the cofactor product S-adenosylhomocysteine (SAH, an inhibitor of SAM-dependent methyltransferases) results in an 8-fold increase in potency against DOT1L, and reduced activities against other protein and non-protein methyltransferases. We solved the crystal structure of DOT1L in complex with Bromo-deaza-SAH and rationalized the observed effects. This discovery reveals a simple strategy to engineer selectivity and potency towards DOT1L into the adenosine scaffold of the cofactor shared by all methyltransferases, and can be exploited towards the development of clinical candidates against mixed lineage leukemia.
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Affiliation(s)
- Wenyu Yu
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - David Smil
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Oleg Fedorov
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Kong T Nguyen
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Yuri Bolshan
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Rima Al-Awar
- Medicinal Chemistry Platform, Ontario Institute for Cancer Research; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 0A3, Canada
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto; 101 College Street, MaRS Centre, South tower, Toronto, Ontario, M5G 1L7, Canada.,Department of Pharmacology and Toxicology; University of Toronto, Toronto, Ontario, Canada
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31
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James LI, Barsyte-Lovejoy D, Zhong N, Krichevsky L, Korboukh VK, Herold JM, MacNevin CJ, Norris JL, Sagum CA, Tempel W, Marcon E, Guo H, Gao C, Huang XP, Duan S, Emili A, Greenblatt JF, Kireev DB, Jin J, Janzen WP, Brown PJ, Bedford MT, Arrowsmith CH, Frye SV. Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol 2013; 9:184-91. [PMID: 23292653 PMCID: PMC3577944 DOI: 10.1038/nchembio.1157] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 11/26/2012] [Indexed: 01/16/2023]
Abstract
We describe the discovery of UNC1215, a potent and selective chemical probe for the methyl-lysine (Kme) reading function of L3MBTL3, a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. UNC1215 binds L3MBTL3 with a Kd of 120 nM, competitively displacing mono- or dimethyl-lysine containing peptides, and is greater than 50-fold selective versus other members of the MBT family while also demonstrating selectivity against more than 200 other reader domains examined. X-ray crystallography identified a novel 2:2 polyvalent mode of interaction. In cells, UNC1215 is non-toxic and binds directly to L3MBTL3 via the Kme-binding pocket of the MBT domains. UNC1215 increases the cellular mobility of GFP-L3MBTL3 fusion proteins and point mutants that disrupt the Kme binding function of GFP-L3MBTL3 phenocopy the effects of UNC1215. Finally, UNC1215 demonstrates a novel Kme-dependent interaction of L3MBTL3 with BCLAF1, a protein implicated in DNA damage repair and apoptosis.
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Affiliation(s)
- Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Tempel W, Dimov S, Tong Y, Park HW, Hong BS. Crystal structure of human multiple copies in T-cell lymphoma-1 oncoprotein. Proteins 2012; 81:519-25. [DOI: 10.1002/prot.24198] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/09/2012] [Accepted: 09/19/2012] [Indexed: 12/20/2022]
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Anastasiou D, Yu Y, Israelsen WJ, Jiang JK, Boxer MB, Hong BS, Tempel W, Dimov S, Shen M, Jha A, Yang H, Mattaini KR, Metallo CM, Fiske BP, Courtney KD, Malstrom S, Khan TM, Kung C, Skoumbourdis AP, Veith H, Southall N, Walsh MJ, Brimacombe KR, Leister W, Lunt SY, Johnson ZR, Yen KE, Kunii K, Davidson SM, Christofk HR, Austin CP, Inglese J, Harris MH, Asara JM, Stephanopoulos G, Salituro FG, Jin S, Dang L, Auld DS, Park HW, Cantley LC, Thomas CJ, Vander Heiden MG. Erratum: Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis. Nat Chem Biol 2012. [DOI: 10.1038/nchembio1212-1008b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Visschedyk D, Rochon A, Tempel W, Dimov S, Park HW, Merrill AR. Certhrax toxin, an anthrax-related ADP-ribosyltransferase from Bacillus cereus. J Biol Chem 2012; 287:41089-102. [PMID: 22992735 DOI: 10.1074/jbc.m112.412809] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We identified Certhrax, the first anthrax-like mART toxin from the pathogenic G9241 strain of Bacillus cereus. Certhrax shares 31% sequence identity with anthrax lethal factor from Bacillus anthracis; however, we have shown that the toxicity of Certhrax resides in the mART domain, whereas anthrax uses a metalloprotease mechanism. Like anthrax lethal factor, Certhrax was found to require protective antigen for host cell entry. This two-domain enzyme was shown to be 60-fold more toxic to mammalian cells than anthrax lethal factor. Certhrax localizes to distinct regions within mouse RAW264.7 cells by 10 min postinfection and is extranuclear in its cellular location. Substitution of catalytic residues shows that the mART function is responsible for the toxicity, and it binds NAD(+) with high affinity (K(D) = 52.3 ± 12.2 μM). We report the 2.2 Å Certhrax structure, highlighting its structural similarities and differences with anthrax lethal factor. We also determined the crystal structures of two good inhibitors (P6 (K(D) = 1.7 ± 0.2 μM, K(i) = 1.8 ± 0.4 μM) and PJ34 (K(D) = 5.8 ± 2.6 μM, K(i) = 9.6 ± 0.3 μM)) in complex with Certhrax. As with other toxins in this family, the phosphate-nicotinamide loop moves toward the NAD(+) binding site with bound inhibitor. These results indicate that Certhrax may be important in the pathogenesis of B. cereus.
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Affiliation(s)
- Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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35
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Nady N, Krichevsky L, Zhong N, Duan S, Tempel W, Amaya MF, Ravichandran M, Arrowsmith CH. Histone recognition by human malignant brain tumor domains. J Mol Biol 2012; 423:702-18. [PMID: 22954662 DOI: 10.1016/j.jmb.2012.08.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/27/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
Abstract
Histone methylation has emerged as an important covalent modification involved in a variety of biological processes, especially regulation of transcription and chromatin dynamics. Lysine methylation is found in three distinct states (monomethylation, dimethylation and trimethylation), which are recognized by specific protein domains. The malignant brain tumor (MBT) domain is one such module found in several chromatin regulatory complexes including Polycomb repressive complex 1. Here, we present a comprehensive characterization of the human MBT family with emphasis on histone binding specificity. SPOT-blot peptide arrays were used to screen for the methyllysine-containing histone peptides that bind to MBT domains found in nine human proteins. Selected interactions were quantified using fluorescence polarization assays. We show that all MBT proteins recognize only monomethyllysine and/or dimethyllysine marks and provide evidence that some MBT domains recognize a defined consensus sequence while others bind in a promiscuous, non-sequence-specific manner. Furthermore, using structure-based mutants, we identify a triad of residues in the methyllysine binding pocket that imparts discrimination between monomethyllysine and dimethyllysine. This study represents a comprehensive analysis of MBT substrate specificity, establishing a foundation for the rational design of selective MBT domain inhibitors that may enable elucidation of their role in human biology and disease.
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Affiliation(s)
- Nataliya Nady
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada M5G 1L7
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36
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Dixon MJ, Gray A, Schenning M, Agacan M, Tempel W, Tong Y, Nedyalkova L, Park HW, Leslie NR, van Aalten DMF, Downes CP, Batty IH. IQGAP proteins reveal an atypical phosphoinositide (aPI) binding domain with a pseudo C2 domain fold. J Biol Chem 2012; 287:22483-96. [PMID: 22493426 PMCID: PMC3391087 DOI: 10.1074/jbc.m112.352773] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/26/2012] [Indexed: 01/22/2023] Open
Abstract
Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP(3)). The binding affinity for PtdInsP(3), together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP(3) effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.
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Affiliation(s)
| | | | | | - Mark Agacan
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, United Kingdom and
| | | | | | | | - Hee-Won Park
- the Structural Genomics Consortium and
- Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
| | | | | | | | - Ian H. Batty
- From the Division of Cell Signalling and Immunology and
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Xu C, Jin J, Bian C, Lam R, Tian R, Weist R, You L, Nie J, Bochkarev A, Tempel W, Tan CS, Wasney GA, Vedadi M, Gish GD, Arrowsmith CH, Pawson T, Yang XJ, Min J. Sequence-specific recognition of a PxLPxI/L motif by an ankyrin repeat tumbler lock. Sci Signal 2012; 5:ra39. [PMID: 22649097 DOI: 10.1126/scisignal.2002979] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ankyrin repeat family A protein 2 (ANKRA2) interacts with the plasma membrane receptor megalin and the class IIa histone deacetylases HDAC4 and HDAC5. We report that the ankyrin repeat domains of ANKRA2 and its close paralog regulatory factor X-associated ankyrin-containing protein (RFXANK) recognize a PxLPxI/L motif found in diverse binding proteins, including HDAC4, HDAC5, HDAC9, megalin, and regulatory factor X, 5 (RFX5). Crystal structures of the ankyrin repeat domain of ANKRA2 in complex with its binding peptides revealed that each of the middle three ankyrin repeats of ANKRA2 recognizes a residue from the PxLPxI/L motif in a tumbler-lock binding mode, with ANKRA2 acting as the lock and the linear binding motif serving as the key. Structural analysis showed that three disease-causing mutations in RFXANK affect residues that are critical for binding to RFX5. These results suggest a fundamental principle of longitudinal recognition of linear sequences by a repeat-type domain. In addition, phosphorylation of serine 350, a residue embedded within the PxLPxI/L motif of HDAC4, impaired the binding of ANKRA2 but generated a high-affinity docking site for 14-3-3 proteins, which may help sequester this HDAC in the cytoplasm. Thus, the binding preference of the PxLPxI/L motif is signal-dependent. Furthermore, proteome-wide screening suggested that a similar phosphorylation-dependent switch may operate in other pathways. Together, our findings uncover a previously uncharacterized sequence- and signal-dependent peptide recognition mode for a repeat-type protein domain.
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Affiliation(s)
- Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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Rothbart SB, Fuchs SM, Nady N, Krajewski K, Tempel W, Xue S, Iberg AN, Barsyte-Lovejoy D, Martinez JY, Bedford MT, Arrowsmith CH, Strahl BD. Abstract 993: A high-throughput peptide array screen of H3K9 methyl effectors identifies UHRF1 as an exception to the “phospho/methyl switch.”. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Increasing evidence suggests that histone post-translational modifications (PTMs) function in combination to regulate the diverse activities associated with chromatin. However, the mechanisms through which multiple histone PTMs influence the association of effector proteins with chromatin is poorly understood. To address this problem, we recently developed a histone peptide array platform containing singly- and multiply-modified histone peptides to examine the binding of chromatin-associated proteins. Using these arrays, we surveyed protein domains that bound methylated H3K9, and uncovered a number of PTM “patterns” that influenced the association with this mark. Interestingly, while most H3K9 methyl binders were ejected by neighboring H3S10 phosphorylation (a PTM enriched in G2/M-phase chromatin), the tandem Tudor domain (TTD) of UHRF1 was insensitive to this known “phospho/methyl switch”. In agreement, structural and biophysical studies confirmed the insensitivity of the UHRF1 TTD to H3S10 phosphorylation. Furthermore, we found that UHRF1 remains bound to chromatin throughout the cell cycle in contrast to HP1, which is ejected from chromatin during mitosis. These results suggest an important role for this ubiquitin ligase during mitosis. Significantly, we further find that the TTD of UHRF1 regulates global DNA methylation, thus definitively linking H3K9me3 binding by UHRF1 to the maintenance of DNA methylation. Taken together, our data suggest that the regulation of DNA methylation by UHRF1 extends beyond S-phase and requires H3K9me3 recognition during mitosis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 993. doi:1538-7445.AM2012-993
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Affiliation(s)
| | | | | | | | | | - Sheng Xue
- 2University of Toronto, Toronto, Ontario, Canada
| | - Aimee N. Iberg
- 3The University of Texas M.D. Anderson Cancer Center, Smithville, TX
| | | | | | - Mark T. Bedford
- 3The University of Texas M.D. Anderson Cancer Center, Smithville, TX
| | | | - Brian D. Strahl
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
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Zhu H, Lee HY, Tong Y, Hong BS, Kim KP, Shen Y, Lim KJ, Mackenzie F, Tempel W, Park HW. Crystal structures of the tetratricopeptide repeat domains of kinesin light chains: insight into cargo recognition mechanisms. PLoS One 2012; 7:e33943. [PMID: 22470497 PMCID: PMC3314626 DOI: 10.1371/journal.pone.0033943] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 02/23/2012] [Indexed: 01/07/2023] Open
Abstract
Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form "a carboxylate clamp" with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.
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Affiliation(s)
- Haizhong Zhu
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Han Youl Lee
- Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada
| | - Yufeng Tong
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Bum-Soo Hong
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Kyung-Phil Kim
- Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada
| | - Yang Shen
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Kyung Jik Lim
- Philip Pocock Catholic Secondary School, Mississauga, Ontario, Canada
| | | | - Wolfram Tempel
- Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Hee-Won Park
- Structural Genomics Consortium, Toronto, Ontario, Canada
- Department of Pharmacology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Adams-Cioaba MA, Li Z, Tempel W, Guo Y, Bian C, Li Y, Lam R, Min J. Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. FEBS Lett 2012; 586:859-65. [PMID: 22449972 DOI: 10.1016/j.febslet.2012.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/01/2012] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
The human PHD finger protein 20 (PHF20) is a putative transcription factor. While little is known about its cognate cellular role, antibodies against PHF20 are present in sera from patients with hepatocellular carcinoma, glioblastoma and childhood medulloblastula. PHF20 comprises two N-terminal Tudor domains, a central C2H2-link zinc finger domain and a C-terminal zinc-binding PHD domain, and is a component of some MLL methyltransferase complexes. Here, we report the crystal structures of the N-terminal Tudor domains of PHF20 and highlight the novel structural features of each domain. We also confirm previous studies suggesting that the second Tudor domain of PHF20 exhibits preference for dimethylated histone substrates.
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Siddiqui N, Tempel W, Nedyalkova L, Volpon L, Wernimont AK, Osborne MJ, Park HW, Borden KLB. Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E. J Mol Biol 2011; 415:781-92. [PMID: 22178476 DOI: 10.1016/j.jmb.2011.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 11/25/2011] [Accepted: 12/01/2011] [Indexed: 01/11/2023]
Abstract
The eukaryotic translation initiation factor eIF4E plays key roles in cap-dependent translation and mRNA export. These functions rely on binding the 7-methyl-guanosine moiety (5'cap) on the 5'-end of all mRNAs. eIF4E is regulated by proteins such as eIF4G and eIF4E binding proteins (4EBPs) that bind the dorsal surface of eIF4E, distal to the cap binding site, and modulate cap binding activity. Both proteins increase the affinity of eIF4E for 5'cap. Our understanding of the allosteric effects and structural underpinnings of 4EBP1 or eIF4G binding can be advanced by obtaining structural data on cap-free eIF4E bound to one of these proteins. Here, we report the crystal structure of apo-eIF4E and cap-free eIF4E in complex with a 4EBP1 peptide. We also monitored 4EBP1 binding to cap-free eIF4E in solution using NMR. Together, these studies suggest that 4EBP1 transforms eIF4E into a cap-receptive state. NMR methods were also used to compare the allosteric routes activated by 4EBP1, eIF4G, and the arenavirus Z protein, a negative regulator of cap binding. We observed chemical shift perturbation at the dorsal binding site leading to alterations in the core of the protein, which were ultimately communicated to the unoccupied cap binding site of eIF4E. There were notable similarities between the routes taken by 4EBP1 and eIF4G and differences from the negative regulator Z. Thus, binding of 4EBP1 or eIF4G allosterically drives alterations throughout the protein that increase the affinity of eIF4E for the 5'cap.
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Affiliation(s)
- Nadeem Siddiqui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada H3T 1J4
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Zhang W, Xu C, Bian C, Tempel W, Crombet L, MacKenzie F, Min J, Liu Z, Qi C. Crystal structure of the Cys2His2-type zinc finger domain of human DPF2. Biochem Biophys Res Commun 2011; 413:58-61. [PMID: 21888896 DOI: 10.1016/j.bbrc.2011.08.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 08/10/2011] [Indexed: 11/29/2022]
Abstract
DPF2 is an evolutionary highly conserved member of the d4-protein family characterized by an N-terminal 2/3 domain, a C2H2-type zinc finger (ZF), and a C-terminal tandem PHD zinc finger. DPF2 is identified as a transcription factor and may be related with some cancers in human. Here, we report the crystal structure of the C2H2-type zinc finger domain of human DPF2 with a canonical C2H2 fold, which contains two beta strands and one alpha helix. Several conserved residues, including Lys207, Lys216 and Arg217, constitute a positively charged surface in C2H2 domain, which implicates that it has the potential to bind DNA. The side chains of the residues Y209, C211, C214, K216, Y218, L224, H227 and H232 form the hydrophobic core of C2H2 domain, which indicates a potential-binding surface in the human DPF2.
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Affiliation(s)
- Wei Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079, People's Republic of China
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Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J. A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. Nat Chem Biol 2011; 7:566-74. [PMID: 21743462 DOI: 10.1038/nchembio.599] [Citation(s) in RCA: 399] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 04/27/2011] [Indexed: 12/12/2022]
Abstract
Protein lysine methyltransferases G9a and GLP modulate the transcriptional repression of a variety of genes via dimethylation of Lys9 on histone H3 (H3K9me2) as well as dimethylation of non-histone targets. Here we report the discovery of UNC0638, an inhibitor of G9a and GLP with excellent potency and selectivity over a wide range of epigenetic and non-epigenetic targets. UNC0638 treatment of a variety of cell lines resulted in lower global H3K9me2 levels, equivalent to levels observed for small hairpin RNA knockdown of G9a and GLP with the functional potency of UNC0638 being well separated from its toxicity. UNC0638 markedly reduced the clonogenicity of MCF7 cells, reduced the abundance of H3K9me2 marks at promoters of known G9a-regulated endogenous genes and disproportionately affected several genomic loci encoding microRNAs. In mouse embryonic stem cells, UNC0638 reactivated G9a-silenced genes and a retroviral reporter gene in a concentration-dependent manner without promoting differentiation.
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Affiliation(s)
- Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
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Liao JCC, Lam R, Brazda V, Duan S, Ravichandran M, Ma J, Xiao T, Tempel W, Zuo X, Wang YX, Chirgadze NY, Arrowsmith CH. Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53. Structure 2011; 19:418-29. [PMID: 21397192 DOI: 10.1016/j.str.2010.12.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Revised: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 02/09/2023]
Abstract
IFI16 is a member of the interferon-inducible HIN-200 family of nuclear proteins. It has been implicated in transcriptional regulation by modulating protein-protein interactions with p53 tumor suppressor protein and other transcription factors. However, the mechanisms of interaction remain unknown. Here, we report the crystal structures of both HIN-A and HIN-B domains of IFI16 determined at 2.0 and 2.35 Å resolution, respectively. Each HIN domain comprises a pair of tightly packed OB-fold subdomains that appear to act as a single unit. We show that both HIN domains of IFI16 are capable of enhancing p53-DNA complex formation and transcriptional activation via distinctive means. HIN-A domain binds to the basic C terminus of p53, whereas the HIN-B domain binds to the core DNA-binding region of p53. Both interactions are compatible with the DNA-bound state of p53 and together contribute to the effect of full-length IFI16 on p53-DNA complex formation and transcriptional activation.
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Affiliation(s)
- Jack C C Liao
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, University Health Network, Toronto, ON M5G 2C4, Canada
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Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J. Structural and histone binding ability characterizations of human PWWP domains. PLoS One 2011; 6:e18919. [PMID: 21720545 PMCID: PMC3119473 DOI: 10.1371/journal.pone.0018919] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 03/24/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. METHODOLOGY/PRINCIPAL FINDINGS The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. CONCLUSIONS PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical β-barrel core, an insertion motif between the second and third β-strands and a C-terminal α-helix bundle. Both the canonical β-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones. ENHANCED VERSION This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.
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Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maria F. Amaya
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wei Qiu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Yanming Wang
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Wang H, Hota PK, Tong Y, Li B, Shen L, Nedyalkova L, Borthakur S, Kim S, Tempel W, Buck M, Park HW. Structural basis of Rnd1 binding to plexin Rho GTPase binding domains (RBDs). J Biol Chem 2011; 286:26093-106. [PMID: 21610070 PMCID: PMC3138255 DOI: 10.1074/jbc.m110.197053] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plexin receptors regulate cell adhesion, migration, and guidance. The Rho GTPase binding domain (RBD) of plexin-A1 and -B1 can bind GTPases, including Rnd1. By contrast, plexin-C1 and -D1 reportedly bind Rnd2 but associate with Rnd1 only weakly. The structural basis of this differential Rnd1 GTPase binding to plexin RBDs remains unclear. Here, we solved the structure of the plexin-A2 RBD in complex with Rnd1 and the structures of the plexin-C1 and plexin-D1 RBDs alone, also compared with the previously determined plexin-B1 RBD.Rnd1 complex structure. The plexin-A2 RBD·Rnd1 complex is a heterodimer, whereas plexin-B1 and -A2 RBDs homodimerize at high concentration in solution, consistent with a proposed model for plexin activation. Plexin-C1 and -D1 RBDs are monomeric, consistent with major residue changes in the homodimerization loop. In plexin-A2 and -B1, the RBD β3-β4 loop adjusts its conformation to allow Rnd1 binding, whereas minimal structural changes occur in Rnd1. The plexin-C1 and -D1 RBDs lack several key non-polar residues at the corresponding GTPase binding surface and do not significantly interact with Rnd1. Isothermal titration calorimetry measurements on plexin-C1 and -D1 mutants reveal that the introduction of non-polar residues in this loop generates affinity for Rnd1. Structure and sequence comparisons suggest a similar mode of Rnd1 binding to the RBDs, whereas mutagenesis suggests that the interface with the highly homologous Rnd2 GTPase is different in detail. Our results confirm, from a structural perspective, that Rnd1 does not play a role in the activation of plexin-C1 and -D1. Plexin functions appear to be regulated by subfamily-specific mechanisms, some of which involve different Rho family GTPases.
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Affiliation(s)
- Hui Wang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
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Davis TL, Walker JR, Campagna-Slater V, Finerty PJ, Paramanathan R, Bernstein G, MacKenzie F, Tempel W, Ouyang H, Lee WH, Eisenmesser EZ, Dhe-Paganon S. Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. PLoS Biol 2010; 8:e1000439. [PMID: 20676357 PMCID: PMC2911226 DOI: 10.1371/journal.pbio.1000439] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 06/16/2010] [Indexed: 11/29/2022] Open
Abstract
Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure∶function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity. Cyclophilins are proteins that catalyze the isomerization of prolines, interconverting this structurally important amino acid between cis and trans isomers. Although there are 17 cyclophilins in the human genome, the function of most cyclophilin isoforms is unknown. At least some members of this protein family are of interest for clinically relevant drug design, as they are targets of the drug cyclosporin, which is used as an immunosuppressant to treat patients following organ transplantation. The absence of a comprehensive picture of the similarities and differences between the different members of this protein family precludes effective and specific drug design, however. In the current study we undertake such a global structure∶function analysis. Using biochemical, structural, and computational methods we characterize the human cyclophilin family in detail and suggest that there is a previously overlooked region of these enzymes that contributes significantly to isoform diversity. We propose that this region may represent an important target for isoform-specific drug design.
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Affiliation(s)
- Tara L. Davis
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - John R. Walker
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Patrick J. Finerty
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ragika Paramanathan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Galina Bernstein
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Farrell MacKenzie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hui Ouyang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- University of Oxford, Headington, United Kingdom
| | - Elan Z. Eisenmesser
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Sirano Dhe-Paganon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Hong BS, Allali-Hassani A, Tempel W, Finerty PJ, MacKenzie F, Dimov S, Vedadi M, Park HW. Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity. J Biol Chem 2010; 285:16330-40. [PMID: 20299452 PMCID: PMC2871500 DOI: 10.1074/jbc.m109.039024] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 02/28/2010] [Indexed: 12/03/2022] Open
Abstract
Human choline kinase (ChoK) catalyzes the first reaction in phosphatidylcholine biosynthesis and exists as ChoKalpha (alpha1 and alpha2) and ChoKbeta isoforms. Recent studies suggest that ChoK is implicated in tumorigenesis and emerging as an attractive target for anticancer chemotherapy. To extend our understanding of the molecular mechanism of ChoK inhibition, we have determined the high resolution x-ray structures of the ChoKalpha1 and ChoKbeta isoforms in complex with hemicholinium-3 (HC-3), a known inhibitor of ChoK. In both structures, HC-3 bound at the conserved hydrophobic groove on the C-terminal lobe. One of the HC-3 oxazinium rings complexed with ChoKalpha1 occupied the choline-binding pocket, providing a structural explanation for its inhibitory action. Interestingly, the HC-3 molecule co-crystallized with ChoKbeta was phosphorylated in the choline binding site. This phosphorylation, albeit occurring at a very slow rate, was confirmed experimentally by mass spectroscopy and radioactive assays. Detailed kinetic studies revealed that HC-3 is a much more potent inhibitor for ChoKalpha isoforms (alpha1 and alpha2) compared with ChoKbeta. Mutational studies based on the structures of both inhibitor-bound ChoK complexes demonstrated that Leu-401 of ChoKalpha2 (equivalent to Leu-419 of ChoKalpha1), or the corresponding residue Phe-352 of ChoKbeta, which is one of the hydrophobic residues neighboring the active site, influences the plasticity of the HC-3-binding groove, thereby playing a key role in HC-3 sensitivity and phosphorylation.
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Affiliation(s)
| | | | | | | | | | | | | | - Hee-Won Park
- From the Structural Genomics Consortium and
- Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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Wernimont AK, Artz JD, Finerty P, Lin Y, Amani M, Allali-Hassani A, Senisterra G, Vedadi M, Tempel W, Mackenzie F, Chau I, Lourido S, Sibley LD, Hui R. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Nat Struct Mol Biol 2010; 17:596-601. [PMID: 20436473 PMCID: PMC3675764 DOI: 10.1038/nsmb.1795] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 03/01/2010] [Indexed: 11/09/2022]
Abstract
Calcium-dependent protein kinases (CDPKs) have pivotal roles in the calcium-signaling pathway in plants, ciliates and apicomplexan parasites and comprise a calmodulin-dependent kinase (CaMK)-like kinase domain regulated by a calcium-binding domain in the C terminus. To understand this intramolecular mechanism of activation, we solved the structures of the autoinhibited (apo) and activated (calcium-bound) conformations of CDPKs from the apicomplexan parasites Toxoplasma gondii and Cryptosporidium parvum. In the apo form, the C-terminal CDPK activation domain (CAD) resembles a calmodulin protein with an unexpected long helix in the N terminus that inhibits the kinase domain in the same manner as CaMKII. Calcium binding triggers the reorganization of the CAD into a highly intricate fold, leading to its relocation around the base of the kinase domain to a site remote from the substrate binding site. This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways.
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Affiliation(s)
- Amy K. Wernimont
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Jennifer D. Artz
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Patrick Finerty
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Y. Lin
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Mehrnaz Amani
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Farrell Mackenzie
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
| | - Sebastian Lourido
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Avenue, St Louis, Missouri 63110, USA. 2Donald Danforth Plant Science Center, 975 N. Warson Road, St Louis, Missouri 63132, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Avenue, St Louis, Missouri 63110, USA. 2Donald Danforth Plant Science Center, 975 N. Warson Road, St Louis, Missouri 63132, USA
| | - Raymond Hui
- Structural Genomics Consortium, University of Toronto, MaRS South Tower, Suite 732, 101 College St., Toronto, Ontario, Canada M5G 1L7
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50
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Wiens CJ, Tong Y, Esmail MA, Oh E, Gerdes JM, Wang J, Tempel W, Rattner JB, Katsanis N, Park HW, Leroux MR. Bardet-Biedl syndrome-associated small GTPase ARL6 (BBS3) functions at or near the ciliary gate and modulates Wnt signaling. J Biol Chem 2010; 285:16218-30. [PMID: 20207729 PMCID: PMC2871489 DOI: 10.1074/jbc.m109.070953] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The expansive family of metazoan ADP-ribosylation factor and ADP-ribosylation factor-like small GTPases is known to play essential roles in modulating membrane trafficking and cytoskeletal functions. Here, we present the crystal structure of ARL6, mutations in which cause Bardet-Biedl syndrome (BBS3), and reveal its unique ring-like localization at the distal end of basal bodies, in proximity to the so-called ciliary gate where vesicles carrying ciliary cargo fuse with the membrane. Overproduction of GDP- or GTP-locked variants of ARL6/BBS3 in vivo influences primary cilium length and abundance. ARL6/BBS3 also modulates Wnt signaling, a signal transduction pathway whose association with cilia in vertebrates is just emerging. Importantly, this signaling function is lost in ARL6 variants containing BBS-associated point mutations. By determining the structure of GTP-bound ARL6/BBS3, coupled with functional assays, we provide a mechanistic explanation for such pathogenic alterations, namely altered nucleotide binding. Our findings therefore establish a previously unknown role for ARL6/BBS3 in mammalian ciliary (dis)assembly and Wnt signaling and provide the first structural information for a BBS protein.
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Affiliation(s)
- Cheryl J Wiens
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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