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Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
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2
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Shi H, Panjikar S, Li C, Ou X, Zhou Y, Zhang K, Song L, Yu R, Sun L, Zhu J. Characterization of a novel recombinant calcium-binding protein from Arca subcrenata and its anti-hepatoma activities in vitro and in vivo. Int J Biol Macromol 2023; 245:125513. [PMID: 37353116 DOI: 10.1016/j.ijbiomac.2023.125513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Previous studies demonstrated that ASP-3 was a novel calcium-binding protein from Arca subcrenata that effectively inhibited the proliferation of HepG2 cells. To further study the antitumor activity and mechanism of ASP-3, the cytotoxic effects of recombinant ASP-3 were evaluated in HepG2 cells. The results demonstrated that ASP-3 inhibited the proliferation of HepG2 cells by competitively binding to the EGF binding pocket of EGFR and inhibiting the JAK-STAT, RAS-RAF-MEK-ERK, and PI3K-Akt-mTOR signaling pathways mediated by EGFR. ASP-3 significantly inhibited tumor growth in a HepG2 cell subcutaneous xenograft nude mouse model, and its (25 mg/kg and 75 mg/kg) tumor inhibition rates were 46.92 % and 60.28 %, respectively. Furthermore, the crystal structure of ASP-3 was resolved at 1.4 Å. ASP-3 formed as a stable dimer and folded as an EF-Hand structure. ASP-3 stably bound to domain I and domain III of the EGFR extracellular region by using molecular docking and molecular dynamics simulation analysis. Compared with the endogenous ligand EGF, ASP-3 displayed a stronger interaction with EGFR. These experimental results indicated that recombinant ASP-3 possessed an effective anti-hepatoma effect. So, it might be a potential molecule for liver cancer therapy.
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Affiliation(s)
- Hui Shi
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | | | - Chunlei Li
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Xiaozheng Ou
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Yun Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kunhao Zhang
- Department of Life Science, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Liyan Song
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China
| | - Rongmin Yu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianhua Zhu
- Biotechnological Institute of Chinese Materia Medica, Jinan University, Guangzhou 510632, China; Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
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3
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Devkota SR, Aryal P, Pokhrel R, Jiao W, Perry A, Panjikar S, Payne RJ, Wilce MCJ, Bhusal RP, Stone MJ. Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins. Nat Commun 2023; 14:4204. [PMID: 37452046 PMCID: PMC10349104 DOI: 10.1038/s41467-023-39879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
Chemokines are key regulators of leukocyte trafficking and attractive targets for anti-inflammatory therapy. Evasins are chemokine-binding proteins from tick saliva, whose application as anti-inflammatory therapeutics will require manipulation of their chemokine target selectivity. Here we describe subclass A3 evasins, which are unique to the tick genus Amblyomma and distinguished from "classical" class A1 evasins by an additional disulfide bond near the chemokine recognition interface. The A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. Unlike A1 evasins, EVA-A was not highly dependent on N- and C-terminal regions to differentiate chemokine targets. Structures of chemokine-bound EVA-A revealed a deep hydrophobic pocket, unique to A3 evasins, that interacts with the residue immediately following the CC motif of the chemokine. Mutations to this pocket altered the chemokine selectivity of EVA-A. Thus, class A3 evasins provide a suitable platform for engineering proteins with applications in research, diagnosis or anti-inflammatory therapy.
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Affiliation(s)
- Shankar Raj Devkota
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Pramod Aryal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Rina Pokhrel
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1142, New Zealand
| | - Andrew Perry
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Santosh Panjikar
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
- Australian Synchrotron, ANSTO, Clayton, VIC, 3168, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ram Prasad Bhusal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
| | - Martin J Stone
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
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Mackie ERR, Barrow AS, Giel MC, Hulett MD, Gendall AR, Panjikar S, Soares da Costa TP. Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity. Commun Biol 2023; 6:550. [PMID: 37217566 DOI: 10.1038/s42003-023-04895-y] [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] [Received: 02/16/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.
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Affiliation(s)
- Emily R R Mackie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Marie-Claire Giel
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark D Hulett
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC, 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, 3086, Australia.
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5
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Hor L, Pilapitiya A, McKenna JA, Panjikar S, Anderson MA, Desvaux M, Paxman JJ, Heras B. Crystal structure of a subtilisin-like autotransporter passenger domain reveals insights into its cytotoxic function. Nat Commun 2023; 14:1163. [PMID: 36859523 PMCID: PMC9977779 DOI: 10.1038/s41467-023-36719-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023] Open
Abstract
Autotransporters (ATs) are a large family of bacterial secreted and outer membrane proteins that encompass a wide range of enzymatic activities frequently associated with pathogenic phenotypes. We present the structural and functional characterisation of a subtilase autotransporter, Ssp, from the opportunistic pathogen Serratia marcescens. Although the structures of subtilases have been well documented, this subtilisin-like protein is associated with a 248 residue β-helix and itself includes three finger-like protrusions around its active site involved in substrate interactions. We further reveal that the activity of the subtilase AT is required for entry into epithelial cells as well as causing cellular toxicity. The Ssp structure not only provides details about the subtilase ATs, but also reveals a common framework and function to more distantly related ATs. As such these findings also represent a significant step forward toward understanding the molecular mechanisms underlying the functional divergence in the large AT superfamily.
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Affiliation(s)
- Lilian Hor
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Akila Pilapitiya
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - James A McKenna
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia
| | - Mickaël Desvaux
- INRAE, Université Clermont Auvergne, UMR454 MEDiS, 63000, Clermont-Ferrand, France
| | - Jason J Paxman
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia.
| | - Begoña Heras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Bundoora, VIC, 3086, Australia.
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6
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Zhong Y, Moghaddas Sani H, Paudel BP, Low JKK, Silva APG, Mueller S, Deshpande C, Panjikar S, Reid XJ, Bedward MJ, van Oijen AM, Mackay JP. The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families. Nat Commun 2022; 13:7524. [PMID: 36473839 PMCID: PMC9726900 DOI: 10.1038/s41467-022-35002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.
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Affiliation(s)
- Yichen Zhong
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Hakimeh Moghaddas Sani
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Bishnu P. Paudel
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Jason K. K. Low
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Ana P. G. Silva
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Stefan Mueller
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Chandrika Deshpande
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Santosh Panjikar
- grid.248753.f0000 0004 0562 0567Australian Synchrotron, Clayton, VIC 3168 Australia ,grid.1002.30000 0004 1936 7857Department of Molecular Biology and Biochemistry, Monash University, Clayton, VIC 3800 Australia
| | - Xavier J. Reid
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Max J. Bedward
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Antoine M. van Oijen
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
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Patel O, Brammananth R, Dai W, Panjikar S, Coppel RL, Lucet IS, Crellin PK. Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis. Acta Crystallogr D Struct Biol 2022; 78:494-508. [PMID: 35362472 PMCID: PMC8972800 DOI: 10.1107/s2059798322001772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
The first crystal structure of the putative cell-wall biosynthesis protein LmcA from Mycobacterium smegmatis is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities, indicating a possible lipid-binding function in lipomannan/lipoarabinomannan biosynthesis. The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one-quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl-myo-inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface-exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full-length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities and one α-helix extending away from the β-barrel core, resembling a ‘cone with a flake’ arrangement. Through xenon derivatization and structural comparison with AlphaFold2-derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from ‘closed’ to ‘open’ conformations, allowing cavity access. An AlphaFold2-derived NCgl2760 model predicted a smaller β-barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis.
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8
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Liu H, Panjikar S, Sheng X, Futamura Y, Zhang C, Shao N, Osada H, Zou H. β-Methyltryptamine Provoking the Crucial Role of Strictosidine Synthase Tyr151-OH for Its Stereoselective Pictet-Spengler Reactions to Tryptoline-type Alkaloids. ACS Chem Biol 2022; 17:187-197. [PMID: 34994203 DOI: 10.1021/acschembio.1c00844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strictosidine synthase (STR), the gate enzyme for monoterpenoid indole alkaloid biosynthesis, catalyzes the Pictet-Spengler reaction (PSR) of various tryptamine derivatives with secologanin assisted by "indole sandwich" stabilization. Continuous exploration with β-methyltryptamine (IPA) stereoselectively delivered the C6-methylstrictosidines and C6-methylvincosides by enzymatic and nonenzymatic PSR, respectively. Unexpectedly, the first "nonindole sandwich" binding mode was witnessed by the X-ray structures of STR1-ligand complexes. Site-directed mutagenesis revealed the critical cryptic role of the hydroxyl group of Tyr151 in IPA biotransformation. Further computational calculations demonstrated the adjustable IPA position in STR1 upon the binding of secologanin, and Tyr151-OH facilitates the productive PSR binding mode via an advantageous hydrogen-bond network. Further chemo-enzymatic manipulation of C6-methylvincosides successfully resulted in the discovered antimalarial framework (IC50 = 0.92 μM).
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Affiliation(s)
- Haicheng Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Santosh Panjikar
- Australia & Department of Molecular Biology and Biochemistry, Monash University, ANSTO, Australian Synchrotron, 800 Blackburn Road, Victoria 3168, Australia
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, & National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chenghua Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, & National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China
- School of Basic Medical Sciences, North Sichuan Medical College, No. 55 Dongshun Road, Gaoping District, Nanchong 637000, China
| | - Nana Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hongbin Zou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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9
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Shahriari S, Sastry M, Panjikar S, Singh Raman RK. Graphene and Graphene Oxide as a Support for Biomolecules in the Development of Biosensors. Nanotechnol Sci Appl 2021; 14:197-220. [PMID: 34815666 PMCID: PMC8605898 DOI: 10.2147/nsa.s334487] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 08/26/2021] [Accepted: 10/02/2021] [Indexed: 01/21/2023] Open
Abstract
Graphene and graphene oxide have become the base of many advanced biosensors due to their exceptional characteristics. However, lack of some properties, such as inertness of graphene in organic solutions and non-electrical conductivity of graphene oxide, are their drawbacks in sensing applications. To compensate for these shortcomings, various methods of modifications have been developed to provide the appropriate properties required for biosensing. Efficient modification of graphene and graphene oxide facilitates the interaction of biomolecules with their surface, and the ultimate bioconjugate can be employed as the main sensing part of the biosensors. Graphene nanomaterials as transducers increase the signal response in various sensing applications. Their large surface area and perfect biocompatibility with lots of biomolecules provide the prerequisite of a stable biosensor, which is the immobilization of bioreceptor on transducer. Biosensor development has paramount importance in the field of environmental monitoring, security, defense, food safety standards, clinical sector, marine sector, biomedicine, and drug discovery. Biosensor applications are also prevalent in the plant biology sector to find the missing links required in the metabolic process. In this review, the importance of oxygen functional groups in functionalizing the graphene and graphene oxide and different types of functionalization will be explained. Moreover, immobilization of biomolecules (such as protein, peptide, DNA, aptamer) on graphene and graphene oxide and at the end, the application of these biomaterials in biosensors with different transducing mechanisms will be discussed.
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Affiliation(s)
- Shiva Shahriari
- Department of Mechanical & Aerospace Engineering, Monash University, Melbourne, Victoria, Australia
| | - Murali Sastry
- Department of Materials Science and Engineering, Monash University, Melbourne, Victoria, Australia
| | - Santosh Panjikar
- ANSTO, Australian Synchrotron, Melbourne, Victoria, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Victoria, Australia
| | - R K Singh Raman
- Department of Mechanical & Aerospace Engineering, Monash University, Melbourne, Victoria, Australia
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10
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Panjikar S. Data evaluation on the fly: Auto-Rickshaw on the MX beamlines of the Australian Synchrotron. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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Paxman J, Vo J, Martínez Ortiz G, Totsika M, Lo A, Hor L, Panjikar S, Schembri M, Heras B. Uncovering the structures and mechanisms for the largest group of bacterial surface virulence factors. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321095787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Soares da Costa TP, Hall CJ, Panjikar S, Wyllie JA, Christoff RM, Bayat S, Hulett MD, Abbott BM, Gendall AR, Perugini MA. Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants. eLife 2021; 10:69444. [PMID: 34313586 PMCID: PMC8341977 DOI: 10.7554/elife.69444] [Citation(s) in RCA: 8] [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: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022] Open
Abstract
Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides with novel modes of action are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. The first class of plant DHDPS inhibitors with micromolar potency against Arabidopsis thaliana DHDPS was identified using a high-throughput chemical screen. We determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. The inhibitors also attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide-resistant weeds.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Jessica A Wyllie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Saadi Bayat
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, Bundoora, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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13
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Subedi P, Paxman JJ, Wang G, Hor L, Hong Y, Verderosa AD, Whitten AE, Panjikar S, Santos-Martin CF, Martin JL, Totsika M, Heras B. Salmonella enterica BcfH Is a Trimeric Thioredoxin-Like Bifunctional Enzyme with Both Thiol Oxidase and Disulfide Isomerase Activities. Antioxid Redox Signal 2021; 35:21-39. [PMID: 33607928 DOI: 10.1089/ars.2020.8218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aims: Thioredoxin (TRX)-fold proteins are ubiquitous in nature. This redox scaffold has evolved to enable a variety of functions, including redox regulation, protein folding, and oxidative stress defense. In bacteria, the TRX-like disulfide bond (Dsb) family mediates the oxidative folding of multiple proteins required for fitness and pathogenic potential. Conventionally, Dsb proteins have specific redox functions with monomeric and dimeric Dsbs exclusively catalyzing thiol oxidation and disulfide isomerization, respectively. This contrasts with the eukaryotic disulfide forming machinery where the modular TRX protein disulfide isomerase (PDI) mediates thiol oxidation and disulfide reshuffling. In this study, we identified and structurally and biochemically characterized a novel Dsb-like protein from Salmonella enterica termed bovine colonization factor protein H (BcfH) and defined its role in virulence. Results: In the conserved bovine colonization factor (bcf) fimbrial operon, the Dsb-like enzyme BcfH forms a trimeric structure, exceptionally uncommon among the large and evolutionary conserved TRX superfamily. This protein also displays very unusual catalytic redox centers, including an unwound α-helix holding the redox active site and a trans-proline instead of the conserved cis-proline active site loop. Remarkably, BcfH displays both thiol oxidase and disulfide isomerase activities contributing to Salmonella fimbrial biogenesis. Innovation and Conclusion: Typically, oligomerization of bacterial Dsb proteins modulates their redox function, with monomeric and dimeric Dsbs mediating thiol oxidation and disulfide isomerization, respectively. This study demonstrates a further structural and functional malleability in the TRX-fold protein family. BcfH trimeric architecture and unconventional catalytic sites permit multiple redox functions emulating in bacteria the eukaryotic PDI dual oxidoreductase activity. Antioxid. Redox Signal. 35, 21-39.
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Affiliation(s)
- Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lilian Hor
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Anthony D Verderosa
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia
| | - Santosh Panjikar
- Macromolecular Crystallography, Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Carlos F Santos-Martin
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Brisbane Innovation Park, Nathan, Australia.,Vice-Chancellor's Unit, University of Wollongong, Wollongong, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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14
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Keough DT, Wun SJ, Baszczyňski O, Eng WS, Špaček P, Panjikar S, Naesens L, Pohl R, Rejman D, Hocková D, Ferrero RL, Guddat LW. Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections. J Med Chem 2021; 64:5710-5729. [PMID: 33891818 DOI: 10.1021/acs.jmedchem.0c02184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori (Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world's population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine-guanine-hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with Ki values as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[(N-3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Shun Jie Wun
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Wai Soon Eng
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton 3168, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Lieve Naesens
- Katholieke Universiteit, Leuven, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Richard L Ferrero
- Hudson Institute of Medical Research, Clayton 3800, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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15
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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16
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Hall CJ, Lee M, Boarder MP, Mangion AM, Gendall AR, Panjikar S, Perugini MA, Soares da Costa TP. Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. FEBS J 2021; 288:4973-4986. [PMID: 33586321 DOI: 10.1111/febs.15766] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/10/2020] [Revised: 01/16/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022]
Abstract
Lysine biosynthesis in plants occurs via the diaminopimelate pathway. The first committed and rate-limiting step of this pathway is catalysed by dihydrodipicolinate synthase (DHDPS), which is allosterically regulated by the end product, l-lysine (lysine). Given that lysine is a common nutritionally limiting amino acid in cereal crops, there has been much interest in probing the regulation of DHDPS. Interestingly, knockouts in Arabidopsis thaliana of each isoform (AtDHDPS1 and AtDHDPS2) result in different phenotypes, despite the enzymes sharing > 85% protein sequence identity. Accordingly, in this study, we compared the catalytic activity, lysine-mediated inhibition and structures of both A. thaliana DHDPS isoforms. We found that although the recombinantly produced enzymes have similar kinetic properties, AtDHDPS1 is 10-fold more sensitive to lysine. We subsequently used X-ray crystallography to probe for structural differences between the apo- and lysine-bound isoforms that could account for the differential allosteric inhibition. Despite no significant changes in the overall structures of the active or allosteric sites, we noted differences in the rotamer conformation of a key allosteric site residue (Trp116) and proposed that this could result in differences in lysine dissociation. Microscale thermophoresis studies supported our hypothesis, with AtDHDPS1 having a ~ 6-fold tighter lysine dissociation constant compared to AtDHDPS2, which agrees with the lower half minimal inhibitory concentration for lysine observed. Thus, we highlight that subtle differences in protein structures, which could not have been predicted from the primary sequences, can have profound effects on the allostery of a key enzyme involved in lysine biosynthesis in plants. DATABASES: Structures described are available in the Protein Data Bank under the accession numbers 6VVH and 6VVI.
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Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Matthew P Boarder
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Alexandra M Mangion
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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17
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Mills S, Aishima J, Aragao D, Caradoc-Davies TT, Cowieson N, Gee CL, Ericsson D, Harrop S, Panjikar S, Smith KML, Riboldi-Tunnicliffe A, Williamson R, Price JR. Crystal structure of posnjakite formed in the first crystal water-cooling line of the ANSTO Melbourne Australian Synchrotron MX1 Double Crystal Monochromator. Acta Crystallogr E Crystallogr Commun 2020; 76:1136-1138. [PMID: 32695467 PMCID: PMC7336798 DOI: 10.1107/s2056989020008099] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 11/10/2022]
Abstract
Exceptionally large crystals of posnjakite, Cu4SO4(OH)6(H2O), formed during corrosion of a Swagelock(tm) Snubber copper gasket within the MX1 beamline at the ANSTO-Melbourne, Australian Synchrotron. The crystal structure was solved using synchrotron radiation to R 1 = 0.029 and revealed a structure based upon [Cu4(OH)6(H2O)O] sheets, which contain Jahn-Teller-distorted Cu octa-hedra. The sulfate tetra-hedra are bonded to one side of the sheet via corner sharing and linked to successive sheets via extensive hydrogen bonds. The sulfate tetra-hedra are split and rotated, which enables additional hydrogen bonds.
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Affiliation(s)
- Stuart Mills
- Geosciences, Museum Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
| | - Jun Aishima
- Brookhaven National Laboratory, 743 Brookhaven Avenue, Upton, NY, USA
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | - David Aragao
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
- Diamond Light Source, Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | | | - Nathan Cowieson
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
- Diamond Light Source, Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | - Christine L. Gee
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel Ericsson
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | - Stephen Harrop
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | - Kate Mary Louise Smith
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | | | - Rachel Williamson
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
| | - Jason Roy Price
- Australian Synchrotron, ANSTO - Melbourne, 800 Blackburn Rd, Clayton, VIC, 3168, Australia
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18
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Impey RE, Lee M, Hawkins DA, Sutton JM, Panjikar S, Perugini MA, Soares da Costa TP. Mis-annotations of a promising antibiotic target in high-priority gram-negative pathogens. FEBS Lett 2020; 594:1453-1463. [PMID: 31943170 DOI: 10.1002/1873-3468.13733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022]
Abstract
The rise of antibiotic resistance combined with the lack of new products entering the market has led to bacterial infections becoming one of the biggest threats to global health. Therefore, there is an urgent need to identify novel antibiotic targets, such as dihydrodipicolinate synthase (DHDPS), an enzyme involved in the production of essential metabolites in cell wall and protein synthesis. Here, we utilised a 7-residue sequence motif to identify mis-annotation of multiple DHDPS genes in the high-priority Gram-negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. We subsequently confirmed these mis-annotations using a combination of enzyme kinetics and X-ray crystallography. Thus, this study highlights the need to ensure genes encoding promising drug targets, like DHDPS, are annotated correctly, especially for clinically important pathogens. PDB ID: 6UE0.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Daniel A Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - J Mark Sutton
- National Infection Service, Research and Development Institute, Public Health England, Salisbury, UK
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, VIC, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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19
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Coombes D, Davies JS, Newton-Vesty MC, Horne CR, Setty TG, Subramanian R, Moir JWB, Friemann R, Panjikar S, Griffin MDW, North RA, Dobson RCJ. The basis for non-canonical ROK family function in the N-acetylmannosamine kinase from the pathogen Staphylococcus aureus. J Biol Chem 2020; 295:3301-3315. [PMID: 31949045 DOI: 10.1074/jbc.ra119.010526] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/08/2019] [Revised: 12/31/2019] [Indexed: 12/31/2022] Open
Abstract
In environments where glucose is limited, some pathogenic bacteria metabolize host-derived sialic acid as a nutrient source. N-Acetylmannosamine kinase (NanK) is the second enzyme of the bacterial sialic acid import and degradation pathway and adds phosphate to N-acetylmannosamine using ATP to prime the molecule for future pathway reactions. Sequence alignments reveal that Gram-positive NanK enzymes belong to the Repressor, ORF, Kinase (ROK) family, but many lack the canonical Zn-binding motif expected for this function, and the sugar-binding EXGH motif is altered to EXGY. As a result, it is unclear how they perform this important reaction. Here, we study the Staphylococcus aureus NanK (SaNanK), which is the first characterization of a Gram-positive NanK. We report the kinetic activity of SaNanK along with the ligand-free, N-acetylmannosamine-bound and substrate analog GlcNAc-bound crystal structures (2.33, 2.20, and 2.20 Å resolution, respectively). These demonstrate, in combination with small-angle X-ray scattering, that SaNanK is a dimer that adopts a closed conformation upon substrate binding. Analysis of the EXGY motif reveals that the tyrosine binds to the N-acetyl group to select for the "boat" conformation of N-acetylmannosamine. Moreover, SaNanK has a stacked arginine pair coordinated by negative residues critical for thermal stability and catalysis. These combined elements serve to constrain the active site and orient the substrate in lieu of Zn binding, representing a significant departure from canonical NanK binding. This characterization provides insight into differences in the ROK family and highlights a novel area for antimicrobial discovery to fight Gram-positive and S. aureus infections.
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Affiliation(s)
- David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Thanuja G Setty
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, KA 560064, India
| | - Ramaswamy Subramanian
- Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India
| | - James W B Moir
- Department of Biology, University of York, Helsington, York YO10 5DD, United Kingdom
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Synchrotron, ANSTO, Victoria 3168, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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20
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Impey RE, Panjikar S, Hall CJ, Bock LJ, Sutton JM, Perugini MA, Soares da Costa TP. Identification of two dihydrodipicolinate synthase isoforms from Pseudomonas aeruginosa that differ in allosteric regulation. FEBS J 2019; 287:386-400. [PMID: 31330085 DOI: 10.1111/febs.15014] [Citation(s) in RCA: 11] [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] [Received: 02/04/2019] [Revised: 06/12/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections, accounting for 10% of all hospital-acquired infections. Current antibiotics against P. aeruginosa are becoming increasingly ineffective due to the exponential rise in drug resistance. Thus, there is an urgent need to validate and characterize novel drug targets to guide the development of new classes of antibiotics against this pathogen. One such target is the diaminopimelate (DAP) pathway, which is responsible for the biosynthesis of bacterial cell wall and protein building blocks, namely meso-DAP and lysine. The rate-limiting step of this pathway is catalysed by the enzyme dihydrodipicolinate synthase (DHDPS), typically encoded for in bacteria by a single dapA gene. Here, we show that P. aeruginosa encodes two functional DHDPS enzymes, PaDHDPS1 and PaDHDPS2. Although these isoforms have similar catalytic activities (kcat = 29 s-1 and 44 s-1 for PaDHDPS1 and PaDHDPS2, respectively), they are differentially allosterically regulated by lysine, with only PaDHDPS2 showing inhibition by the end product of the DAP pathway (IC50 = 130 μm). The differences in allostery are attributed to a single amino acid difference in the allosteric binding pocket at position 56. This is the first example of a bacterium that contains multiple bona fide DHDPS enzymes, which differ in allosteric regulation. We speculate that the presence of the two isoforms allows an increase in the metabolic flux through the DAP pathway when required in this clinically important pathogen. DATABASES: PDB ID: 6P90.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lucy J Bock
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - J Mark Sutton
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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21
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Cai Y, Shao N, Xie H, Futamura Y, Panjikar S, Liu H, Zhu H, Osada H, Zou H. Stereocomplementary Chemoenzymatic Pictet–Spengler Reactions for Formation of Rare Azepino-indole Frameworks: Discovery of Antimalarial Compounds. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01628] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yunrui Cai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Nana Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Hujun Xie
- Department of Applied Chemistry, Zhejiang Gongshang University, Hangzhou 310035, People’s Republic of China
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Santosh Panjikar
- ANSTO, Australian Synchrotron, 800 Blackburn Road, Victoria 3168, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Victoria 3800, Australia
| | - Haicheng Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Huajian Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hongbin Zou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People’s Republic of China
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22
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Truong JQ, Panjikar S, Shearwin-Whyatt L, Bruning JB, Shearwin KE. Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68. Acta Crystallogr D Struct Biol 2019; 75:670-681. [PMID: 31282476 DOI: 10.1107/s2059798319009008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/24/2019] [Indexed: 11/11/2022]
Abstract
Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.
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Affiliation(s)
- Jia Quyen Truong
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Santosh Panjikar
- MX, Australian Synchrotron, 800 Blackburn Road Clayton, Melbourne, VIC 3168, Australia
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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23
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Paxman JJ, Lo AW, Sullivan MJ, Panjikar S, Kuiper M, Whitten AE, Wang G, Luan CH, Moriel DG, Tan L, Peters KM, Phan MD, Gee CL, Ulett GC, Schembri MA, Heras B. Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules. Nat Commun 2019; 10:1967. [PMID: 31036849 PMCID: PMC6488583 DOI: 10.1038/s41467-019-09814-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 02/13/2019] [Accepted: 03/28/2019] [Indexed: 12/31/2022] Open
Abstract
Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.
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Affiliation(s)
- Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Matthew J Sullivan
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, 4222, QLD, Australia
| | - Santosh Panjikar
- Macromolecular Crystallography, Australian Synchrotron, Clayton, 3168, VIC, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, 3800, VIC, Australia
| | - Michael Kuiper
- Molecular & Materials Modelling group Data61, CSIRO, Docklands, Melbourne, 8012, VIC, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, 2234, NSW, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia
| | - Chi-Hao Luan
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Chicago, 60208, IL, USA
| | - Danilo G Moriel
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Kate M Peters
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Christine L Gee
- Macromolecular Crystallography, Australian Synchrotron, Clayton, 3168, VIC, Australia
| | - Glen C Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, 4222, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia.
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24
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Zhang Y, Panjikar S, Chen K, Karatchevtseva I, Tao Z, Wei G. Lanthanoid Heteroleptic Complexes with Cucurbit[5]uril and Dicarboxylate Ligands: From Discrete Structures to One-Dimensional and Two-Dimensional Polymers. Inorg Chem 2019; 58:506-515. [PMID: 30557010 DOI: 10.1021/acs.inorgchem.8b02732] [Citation(s) in RCA: 8] [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] [Indexed: 01/03/2023]
Abstract
Lanthanoid heteroleptic complexes with cucurbit[5]uril {Q[5]} and two dicarboxylate ligands, e.g., diglycolic acid (H2DGC) and glutaric acid (H2GT), have been investigated with six new compounds featuring a tetrametallic and dimetallic discrete structures, a one-dimensional (1D) polymer, and three two-dimensional (2D) polymers with a unique honeycomb-type topology being synthesized and structurally characterized. [La4(Q[5])3(DGC)2(NO3)2(H2O)12][La(DGC)(H2O)6]·7NO3· nH2O (1) has a tetrametallic structure constructed with three bis-bidentate Q[5] ligands linking two [La(DGC)(H2O)2]+ species in the middle and two [La(H2O)4(NO3)]2+ species at both ends. [Ce2(Q[5])(DGC)(NO3)(H2O)10]·3NO3·4H2O (2) has a dimetallic structure built up with a bis-bidentate Q[5] ligand linking [Ce(DGC)(H2O)3(NO3)] and [Ce(H2O)7]3+ on each side of the Q[5] portals. [Ce3(Q[5])3(DGC)2(H2O)9][Ce(DGC)(H2O)6]2·7NO3· nH2O (3) has a 1D polymeric structure built up with bis-bidentate Q[5] ligands in-turn linking one [Ce(H2O)6]3+ and two [Ce(DGC)(H2O)6]1+ cationic species. [Ln2(Q[5])2(GT)(H2O)6]·4NO3· nH2O [Ln = La (4), Ce (5) and Nd (6)] have similar 2D polymeric structures built up with two types of 9-fold coordinated Ln polyhedra linked by Q[5] via bis-bidentate carbonyl groups on both sides forming 1D chains which are further connected by bridging GT2- ligands to form 2D polymers with a unique honeycomb-type topology. Their vibrational modes and electronic structures have also been investigated.
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Affiliation(s)
- Yingjie Zhang
- Nuclear Fuel Cycle Research Theme , Australian Nuclear Science and Technology Organisation , Locked Bag 2001 , Kirrawee DC , New South Wales 2232 , Australia
| | - Santosh Panjikar
- Australian Synchrotron , 800 Blackburn Road , Clayton , Victoria 3168 , Australia
| | - Kai Chen
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering , Nanjing University of Information Science & Technology , Nanjing 210044 , P. R. China
| | - Inna Karatchevtseva
- Nuclear Fuel Cycle Research Theme , Australian Nuclear Science and Technology Organisation , Locked Bag 2001 , Kirrawee DC , New South Wales 2232 , Australia
| | - Zhu Tao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province , Guizhou University , Guiyang , Guizhou 550025 , P. R. China
| | - Gang Wei
- CSIRO Manufacturing , P.O. Box 218, Lindfield , New South Wales 2070 , Australia
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25
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Abstract
Benzene and its derivatives form a class of priority pollutants whose exposure poses grave risk to human health. Since benzene lacks active functional groups, devising specific sensors for its direct detection from a milieu of aromatics has remained a daunting task. Here, we report three engineered protein-based biosensors that exclusively and specifically detect benzene and its derivatives up to a detection limit of 0.3 ppm. Further, the biosensor design has been engineered to create templates that possess the ability to specifically discriminate between alkyl substituted benzene derivatives; such as toluene, m-xylene, and mesitylene. Interference tests with simulated wastewater samples reveal that the engineered biosensors can selectively detect a specific benzene compound in water samples containing a milieu of high concentrations of commonly occurring pollutants. This work demonstrates the potential of structure guided protein engineering as a competent strategy toward design of selective biosensors for direct detection of benzene group of pollutants from real time environmental samples.
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Affiliation(s)
- Shamayeeta Ray
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra India
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
- Australian Synchrotron, Victoria 3168, Australia
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra India
- Wadhwani Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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26
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Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC. Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3. Nat Commun 2018; 9:3732. [PMID: 30213934 PMCID: PMC6137059 DOI: 10.1038/s41467-018-06096-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/15/2018] [Indexed: 11/18/2022] Open
Abstract
Conjugation is fundamental for the acquisition of new genetic traits and the development of antibiotic resistance in pathogenic organisms. Here, we show that a hypothetical Clostridium perfringens protein, TcpK, which is encoded by the tetracycline resistance plasmid pCW3, is essential for efficient conjugative DNA transfer. Our studies reveal that TcpK is a member of the winged helix-turn-helix (wHTH) transcription factor superfamily and that it forms a dimer in solution. Furthermore, TcpK specifically binds to a nine-nucleotide sequence that is present as tandem repeats within the pCW3 origin of transfer (oriT). The X-ray crystal structure of the TcpK–TcpK box complex reveals a binding mode centered on and around the β-wing, which is different from what has been previously shown for other wHTH proteins. Structure-guided mutagenesis experiments validate the specific interaction between TcpK and the DNA molecule. Additional studies highlight that the TcpK dimer is important for specific DNA binding. Conjugative transfer of antibiotic resistance plasmid pCW3 in Clostridium perfringens is mediated by the tcp locus. Here, the authors identify a wHTH-type protein, TcpK, that is essential for efficient plasmid transfer and interacts with the plasmid oriT region in a unique manner.
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Affiliation(s)
- Daouda A K Traore
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.,Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako (USTTB), BP E3206, Bamako, Mali
| | - Jessica A Wisniewski
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Paul J Conroy
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.,Australian Synchrotron, Clayton, 3168, VIC, Australia
| | - Yee-Foong Mok
- Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia
| | - Carmen Lao
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia
| | - Michael D W Griffin
- Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia
| | - Vicki Adams
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.
| | - Julian I Rood
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia.
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800, VIC, Australia. .,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, 3800, VIC, Australia. .,EMBL Australia, Monash University, Clayton, 3800, VIC, Australia.
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27
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Carrasco-López C, Ferreira JC, Lui NM, Schramm S, Berraud-Pache R, Navizet I, Panjikar S, Naumov P, Rabeh WM. Beetle luciferases with naturally red- and blue-shifted emission. Life Sci Alliance 2018; 1:e201800072. [PMID: 30456363 PMCID: PMC6238593 DOI: 10.26508/lsa.201800072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 04/23/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 01/23/2023] Open
Abstract
New crystal structures of red- and green blue–shifted beetle luciferases reveal that the color emission mechanism is dependent on the active site microenvironment affected by the conformation of loop regions. The different colors of light emitted by bioluminescent beetles that use an identical substrate and chemiexcitation reaction sequence to generate light remain a challenging and controversial mechanistic conundrum. The crystal structures of two beetle luciferases with red- and blue-shifted light relative to the green yellow light of the common firefly species provide direct insight into the molecular origin of the bioluminescence color. The structure of a blue-shifted green-emitting luciferase from the firefly Amydetes vivianii is monomeric with a structural fold similar to the previously reported firefly luciferases. The only known naturally red-emitting luciferase from the glow-worm Phrixothrix hirtus exists as tetramers and octamers. Structural and computational analyses reveal varying aperture between the two domains enclosing the active site. Mutagenesis analysis identified two conserved loops that contribute to the color of the emitted light. These results are expected to advance comparative computational studies into the conformational landscape of the luciferase reaction sequence.
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Affiliation(s)
| | | | - Nathan M Lui
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefan Schramm
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Romain Berraud-Pache
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, Marne-la-Vallée, France
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, Marne-la-Vallée, France
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Panče Naumov
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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28
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Aragão D, Aishima J, Cherukuvada H, Clarken R, Clift M, Cowieson NP, Ericsson DJ, Gee CL, Macedo S, Mudie N, Panjikar S, Price JR, Riboldi-Tunnicliffe A, Rostan R, Williamson R, Caradoc-Davies TT. MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron. J Synchrotron Radiat 2018; 25:885-891. [PMID: 29714201 PMCID: PMC5929359 DOI: 10.1107/s1600577518003120] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/22/2018] [Indexed: 05/12/2023]
Abstract
MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8-21 keV to a focal spot of 22 × 12 µm FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s-1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The beamline is now mature and has enjoyed a full user program for the last nine years. This paper describes the beamline status, plans for its future and some recent scientific highlights.
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Affiliation(s)
- David Aragão
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Jun Aishima
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton Campus, Clayton, Victoria 3168, Australia
| | - Hima Cherukuvada
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Robert Clarken
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Mark Clift
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Nathan Philip Cowieson
- B21 SAXS, Diamond Light Source Ltd, Hartwell Science and Innovation Campus, Didcot OX11 0DE, England
| | | | - Christine L. Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA
| | - Sofia Macedo
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Nathan Mudie
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Jason Roy Price
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | | | - Robert Rostan
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Rachel Williamson
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia
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29
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Paxman JJ, Lo A, Panjikar S, Kuiper M, Luan C, Schembri M, Heras B. NEW STRUCTURAL FEATURES REVEAL HOW BACTERIA STICK TO HOST SURFACES. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.652.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jason John Paxman
- Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneAustralia
| | - Alvin Lo
- Chemistry and Molecular SciencesAustralian Infectious Diseases Research CentreBrisbaneAustralia
| | - Santosh Panjikar
- Macromolecular CrystallographyAustralian SynchrotronMelbourneAustralia
| | - Mike Kuiper
- Molecular and Materials Modelling group Data61CSIROMelbourneAustralia
| | - Chi‐Hao Luan
- Molecular BiosciencesNorthwestern UniversityChicagoIL
| | - Mark Schembri
- Chemistry and Molecular SciencesAustralian Infectious Diseases Research CentreBrisbaneAustralia
| | - Begoña Heras
- Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneAustralia
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30
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Soares da Costa TP, Abbott BM, Gendall AR, Panjikar S, Perugini MA. Molecular evolution of an oligomeric biocatalyst functioning in lysine biosynthesis. Biophys Rev 2018; 10:153-162. [PMID: 29204887 PMCID: PMC5899710 DOI: 10.1007/s12551-017-0350-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 12/28/2022] Open
Abstract
Dihydrodipicolinate synthase (DHDPS) is critical to the production of lysine through the diaminopimelate (DAP) pathway. Elucidation of the function, regulation and structure of this key class I aldolase has been the focus of considerable study in recent years, given that the dapA gene encoding DHDPS has been found to be essential to bacteria and plants. Allosteric inhibition by lysine is observed for DHDPS from plants and some bacterial species, the latter requiring a histidine or glutamate at position 56 (Escherichia coli numbering) over a basic amino acid. Structurally, two DHDPS monomers form the active site, which binds pyruvate and (S)-aspartate β-semialdehyde, with most dimers further dimerising to form a tetrameric arrangement around a solvent-filled centre cavity. The architecture and behaviour of these dimer-of-dimers is explored in detail, including biophysical studies utilising analytical ultracentrifugation, small-angle X-ray scattering and macromolecular crystallography that show bacterial DHDPS tetramers adopt a head-to-head quaternary structure, compared to the back-to-back arrangement observed for plant DHDPS enzymes. Finally, the potential role of pyruvate in providing substrate-mediated stabilisation of DHDPS is considered.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Melbourne, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC, 3800, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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31
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Bhaskar S, Panjikar S, Anand R. Crystallographic analysis of β-ketoadipyl-CoA thiolase from Psedomonas putida. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317093238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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33
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Ray S, Panjikar S, Anand R. Structure-guided design of aromatic biosensors for water quality monitoring. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317094748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Patel O, Griffin MDW, Panjikar S, Dai W, Ma X, Chan H, Zheng C, Kropp A, Murphy JM, Daly RJ, Lucet IS. Structure of SgK223 pseudokinase reveals novel mechanisms of homotypic and heterotypic association. Nat Commun 2017; 8:1157. [PMID: 29079850 PMCID: PMC5660093 DOI: 10.1038/s41467-017-01279-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 09/01/2017] [Indexed: 12/26/2022] Open
Abstract
The mammalian pseudokinase SgK223, and its structurally related homologue SgK269, are oncogenic scaffolds that nucleate the assembly of specific signalling complexes and regulate tyrosine kinase signalling. Both SgK223 and SgK269 form homo- and hetero-oligomers, a mechanism that underpins a diversity of signalling outputs. However, mechanistic insights into SgK223 and SgK269 homo- and heterotypic association are lacking. Here we present the crystal structure of SgK223 pseudokinase domain and its adjacent N- and C-terminal helices. The structure reveals how the N- and C-regulatory helices engage in a novel fold to mediate the assembly of a high-affinity dimer. In addition, we identified regulatory interfaces on the pseudokinase domain required for the self-assembly of large open-ended oligomers. This study highlights the diversity in how the kinase fold mediates non-catalytic functions and provides mechanistic insights into how the assembly of these two oncogenic scaffolds is achieved in order to regulate signalling output. Pseudokinases lack kinase activity, yet they impact cellular physiology through the regulation of bona fide signaling kinases. Here the authors describe the structure of the SgK223 pseudokinase and its adjacent domains, and identify regulatory interfaces required for self-assembly and downstream signaling.
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Affiliation(s)
- Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, VIC, 3168, Australia.,Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, Clayton, VIC, 3800, Australia
| | - Weiwen Dai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Xiuquan Ma
- Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, Clayton, VIC, 3800, Australia.,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Howard Chan
- Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, Clayton, VIC, 3800, Australia.,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Celine Zheng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashleigh Kropp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Roger J Daly
- Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, Clayton, VIC, 3800, Australia.,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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35
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Ray S, Maitra A, Biswas A, Panjikar S, Mondal J, Anand R. Functional insights into the mode of DNA and ligand binding of the TetR family regulator TylP from Streptomyces fradiae. J Biol Chem 2017; 292:15301-15311. [PMID: 28739805 DOI: 10.1074/jbc.m117.788000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 03/23/2017] [Revised: 07/21/2017] [Indexed: 01/18/2023] Open
Abstract
Tetracycline repressors (TetRs) modulate multidrug efflux pathways in several pathogenic bacteria. In Streptomyces, they additionally regulate secondary metabolic pathways like antibiotic production. For instance, in the antibiotic producer Streptomyces fradiae, a layered network of TetRs regulates the levels of the commercially important antibiotic tylosin, with TylP occupying the top of this cascading network. TetRs exist in two functional states, the DNA-bound and the ligand-bound form, which are allosterically regulated. Here, to develop deeper insights into the factors that govern allostery, the crystal structure of TylP was solved to a resolution of 2.3 Å. The structure revealed that TylP possesses several unique features; notably, it harbors a unique C-terminal helix-loop extension that spans the entire length of the structure. This anchor connects the DNA-binding domain (DBD) with the ligand-binding domain (LBD) via a mix of positively charged and hydrogen-bonding interactions. Supporting EMSA studies with a series of ΔC truncated versions show that a systematic deletion of this region results in complete loss of DNA binding. The structure additionally revealed that TylP is markedly different in the orientation of its DBD and LBD architecture and the dimeric geometry from its hypothesized Streptomyces homologue CprB, which is a γ-butyrolactone regulator. Rather, TylP is closer in structural design to macrolide-binding TetRs found in pathogens. Supporting molecular dynamic studies suggested that TylP binds a macrolide intermediate in the tylosin pathway. Collectively, the structure along with corroborating biochemical studies provided insights into the novel mode of regulation of TetRs in antibiotic-producing organisms.
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Affiliation(s)
- Shamayeeta Ray
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India.,the IITB-Monash Research Academy, Mumbai-400076, India
| | - Anwesha Maitra
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Anwesha Biswas
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Santosh Panjikar
- the Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.,the Australian Synchrotron, Victoria 3168, Australia, and
| | - Jagannath Mondal
- the Tata Institute of Fundamental Research (TIFR) Centre for Interdisciplinary Sciences, Hyderabad-500075, India
| | - Ruchi Anand
- From the Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India,
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Abstract
Phenolic aromatic compounds are a major source of environmental pollution. Currently there are no in situ methods for specifically and selectively detecting these pollutants. Here, we exploit the nature's biosensory machinery by employing Acinetobacter calcoaceticus NCIB8250 protein, MopR, as a model system to develop biosensors for selective detection of a spectrum of these pollutants. The X-ray structure of the sensor domain of MopR was used as a scaffold for logic-based tunable biosensor design. By employing a combination of in silico structure guided approaches, mutagenesis and isothermal calorimetric studies, we were able to generate biosensor templates, that can selectively and specifically sense harmful compounds like chlorophenols, cresols, catechol, and xylenols. Furthermore, the ability of native protein to selectively sense phenol as the primary ligand was also enhanced. Overall, this methodology can be extended as a suitable framework for development of a series of exclusive biosensors for accurate and selective detection of aromatic pollutants from real time environmental samples.
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Affiliation(s)
- Shamayeeta Ray
- IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Santosh Panjikar
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra India
- Wadhwani
Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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37
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Christensen JB, Soares da Costa TP, Faou P, Pearce FG, Panjikar S, Perugini MA. Structure and Function of Cyanobacterial DHDPS and DHDPR. Sci Rep 2016; 6:37111. [PMID: 27845445 PMCID: PMC5109050 DOI: 10.1038/srep37111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 11/21/2022] Open
Abstract
Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.
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Affiliation(s)
- Janni B. Christensen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - T. P. Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - F. Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Victoria 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
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38
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Weiss MS, Diederichs K, Read RJ, Panjikar S, Van Duyne GD, Matera AG, Fischer U, Grimm C. A critical examination of the recently reported crystal structures of the human SMN protein. Hum Mol Genet 2016; 25:4717–4725. [PMID: 27577872 PMCID: PMC5418738 DOI: 10.1093/hmg/ddw298] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
A recent publication by Seng et al. in this journal reports the crystallographic structure of refolded, full-length SMN protein and two disease-relevant derivatives thereof. Here, we would like to suggest that at least two of the structures reported in that study are incorrect. We present evidence that one of the associated crystallographic datasets is derived from a crystal of the bacterial Sm-like protein Hfq and that a second dataset is derived from a crystal of the bacterial Gab protein. Both proteins are frequent contaminants of bacterially overexpressed proteins which might have been co-purified during metal affinity chromatography. A third structure presented in the Seng et al. paper cannot be examined further because neither the atomic coordinates, nor the diffraction intensities were made publicly available. The Tudor domain protein SMN has been shown to be a component of the SMN complex, which mediates the assembly of RNA-protein complexes of uridine-rich small nuclear ribonucleoproteins (UsnRNPs). Importantly, this activity is reduced in SMA patients, raising the possibility that the aetiology of SMA is linked to RNA metabolism. Structural studies on diverse components of the SMN complex, including fragments of SMN itself have contributed greatly to our understanding of the cellular UsnRNP assembly machinery. Yet full-length SMN has so far evaded structural elucidation. The Seng et al. study claimed to have closed this gap, but based on the results presented here, the only conclusion that can be drawn is that the Seng et al. study is largely invalid and should be retracted from the literature.
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Affiliation(s)
- Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | | | - Randy J Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
| | | | | | | | - Utz Fischer
- Departement of Biochemistry, Biocenter of the University, University of Wuerzburg, Würzburg, Germany
| | - Clemens Grimm
- Departement of Biochemistry, Biocenter of the University, University of Wuerzburg, Würzburg, Germany
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39
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Ray S, Panjikar S, Anand R. Structural basis of selective aromatic pollutant sensing by MopR, an NtrC family transcriptional regulator. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316096182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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40
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Ray S, Gunzburg MJ, Wilce M, Panjikar S, Anand R. Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator. ACS Chem Biol 2016; 11:2357-65. [PMID: 27362503 DOI: 10.1021/acschembio.6b00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivo biosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopR(AB)) from Acinetobacter calcoaceticus in complex with phenol and its derivatives to a maximum resolution of 2.5 Å. The structure reveals that the N-terminal residues 21-47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the "nitric oxide signaling and golgi transport" fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopR(AB) nests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.
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Affiliation(s)
- Shamayeeta Ray
- IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Menachem J. Gunzburg
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew Wilce
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Santosh Panjikar
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
- Wadhwani
Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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41
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Nazmi AR, Lang EJM, Bai Y, Allison TM, Othman MH, Panjikar S, Arcus VL, Parker EJ. Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate. J Biol Chem 2016; 291:21836-21847. [PMID: 27502275 DOI: 10.1074/jbc.m116.741637] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 06/02/2016] [Revised: 07/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DAH7PS operates at the start of the biosynthetic pathway for aromatic metabolites, whereas CM operates in a dedicated branch of the pathway for the biosynthesis of amino acids tyrosine and phenylalanine. In line with sequence predictions, the two catalytic functions are located in distinct domains, and these two activities can be separated and retain functionality. For the full-length protein, prephenate, the product of the CM reaction, acts as an allosteric inhibitor for the DAH7PS. The crystal structure of the full-length protein with prephenate bound and the accompanying small angle x-ray scattering data reveal the molecular mechanism of the allostery. Prephenate binding results in the tighter association between the dimeric CM domains and the tetrameric DAH7PS, occluding the active site and therefore disrupting DAH7PS function. Acquisition of a physical gating mechanism to control catalytic function through gene fusion appears to be a general mechanism for providing allostery for this enzyme.
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Affiliation(s)
- Ali Reza Nazmi
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Eric J M Lang
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Yu Bai
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Timothy M Allison
- the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Mohamad H Othman
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- the Australian Synchrotron, Clayton, Melbourne, Victoria 3168, Australia.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Vickery L Arcus
- the School of Science, University of Waikato, Hamilton 3240, New Zealand, and
| | - Emily J Parker
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
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Soares da Costa TP, Desbois S, Dogovski C, Gorman MA, Ketaren NE, Paxman JJ, Siddiqui T, Zammit LM, Abbott BM, Robins-Browne RM, Parker MW, Jameson GB, Hall NE, Panjikar S, Perugini MA. Structural Determinants Defining the Allosteric Inhibition of an Essential Antibiotic Target. Structure 2016; 24:1282-1291. [PMID: 27427481 DOI: 10.1016/j.str.2016.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/22/2016] [Accepted: 05/06/2016] [Indexed: 11/29/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine biosynthesis pathway of bacteria. The pathway can be regulated by feedback inhibition of DHDPS through the allosteric binding of the end product, lysine. The current dogma states that DHDPS from Gram-negative bacteria are inhibited by lysine but orthologs from Gram-positive species are not. The 1.65-Å resolution structure of the Gram-negative Legionella pneumophila DHDPS and the 1.88-Å resolution structure of the Gram-positive Streptococcus pneumoniae DHDPS bound to lysine, together with comprehensive functional analyses, show that this dogma is incorrect. We subsequently employed our crystallographic data with bioinformatics, mutagenesis, enzyme kinetics, and microscale thermophoresis to reveal that lysine-mediated inhibition is not defined by Gram staining, but by the presence of a His or Glu at position 56 (Escherichia coli numbering). This study has unveiled the molecular determinants defining lysine-mediated allosteric inhibition of bacterial DHDPS.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Con Dogovski
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Natalia E Ketaren
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Tanzeela Siddiqui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Leanne M Zammit
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia; Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Geoffrey B Jameson
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Nathan E Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, VIC 3168, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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43
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Titelbild: Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily (Angew. Chem. 28/2016). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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44
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Cover Picture: Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily (Angew. Chem. Int. Ed. 28/2016). Angew Chem Int Ed Engl 2016. [DOI: 10.1002/anie.201604250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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45
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Mittelstädt G, Moggré GJ, Panjikar S, Nazmi AR, Parker EJ. Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail. Protein Sci 2016; 25:1492-506. [PMID: 27191057 DOI: 10.1002/pro.2948] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/08/2016] [Accepted: 05/11/2016] [Indexed: 02/03/2023]
Abstract
Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first committed step of the histidine biosynthesis in plants and microorganisms. Here, we present the functional and structural characterization of the ATP-PRT from the pathogenic ε-proteobacteria Campylobacter jejuni (CjeATP-PRT). This enzyme is a member of the long form (HisGL ) ATP-PRT and is allosterically inhibited by histidine, which binds to a remote regulatory domain, and competitively inhibited by AMP. In the crystalline form, CjeATP-PRT was found to adopt two distinctly different hexameric conformations, with an open homohexameric structure observed in the presence of substrate ATP, and a more compact closed form present when inhibitor histidine is bound. CjeATP-PRT was observed to adopt only a hexameric quaternary structure in solution, contradicting previous hypotheses favoring an allosteric mechanism driven by an oligomer equilibrium. Instead, this study supports the conclusion that the ATP-PRT long form hexamer is the active species; the tightening of this structure in response to remote histidine binding results in an inhibited enzyme.
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Affiliation(s)
- Gerd Mittelstädt
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Christchurch, 8140, New Zealand.,Department of Chemistry, University of Canterbury, Christchurch, 8140, New Zealand
| | - Gert-Jan Moggré
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Christchurch, 8140, New Zealand.,Department of Chemistry, University of Canterbury, Christchurch, 8140, New Zealand
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Melbourne, Victoria, 3168, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Campus, Melbourne, Victoria, 3800, Australia
| | - Ali Reza Nazmi
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Christchurch, 8140, New Zealand.,Department of Chemistry, University of Canterbury, Christchurch, 8140, New Zealand
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46
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Knott GJ, Panjikar S, Thorn A, Fox AH, Conte MR, Lee M, Bond CS. A crystallographic study of human NONO (p54(nrb)): overcoming pathological problems with purification, data collection and noncrystallographic symmetry. Acta Crystallogr D Struct Biol 2016; 72:761-9. [PMID: 27303796 DOI: 10.1107/s2059798316005830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/08/2016] [Indexed: 12/19/2022]
Abstract
Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54(nrb)) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conserved Drosophila behaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators. However, work with the NONO homodimer has been limited by rapid irreversible sample aggregation. Here, it is reported that L-proline stabilizes purified NONO homodimers, enabling good-quality solution small-angle X-ray structure determination and crystallization. NONO crystallized in the apparent space group P21 with a unique axis (b) of 408.9 Å and with evidence of twinning, as indicated by the cumulative intensity distribution L statistic, suggesting the possibility of space group P1. Structure solution by molecular replacement shows a superhelical arrangement of six NONO homodimers (or 12 in P1) oriented parallel to the long axis, resulting in extensive noncrystallographic symmetry. Further analysis revealed that the crystal was not twinned, but the collected data suffered from highly overlapping reflections that obscured the L-test. Optimized data collection on a new crystal using higher energy X-rays, a smaller beam width and an increased sample-to-detector distance produced non-overlapping reflections to 2.6 Å resolution. The steps taken to analyse and overcome this series of practical difficulties and to produce a biologically informative structure are discussed.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | | | - Andrea Thorn
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, England
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
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47
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily. Angew Chem Int Ed Engl 2016; 55:7930-3. [DOI: 10.1002/anie.201602719] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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48
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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49
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Busby JN, Lott JS, Panjikar S. Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure. Acta Crystallogr D Struct Biol 2016; 72:182-91. [PMID: 26894666 DOI: 10.1107/s2059798315023566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022]
Abstract
The B and C proteins from the ABC toxin complex of Yersinia entomophaga form a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12 data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used in Auto-Rickshaw for multiple rounds of autobuilding and MRSAD.
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Affiliation(s)
- Jason Nicholas Busby
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Santosh Panjikar
- MX, Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, VIC 3168, Australia
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50
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Watson GM, Gunzburg MJ, Ambaye ND, Lucas WAH, Traore DA, Kulkarni K, Cergol KM, Payne RJ, Panjikar S, Pero SC, Perlmutter P, Wilce MCJ, Wilce JA. Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target. J Med Chem 2015; 58:7707-18. [DOI: 10.1021/acs.jmedchem.5b00609] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | | | | | | | | | - Katie M. Cergol
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Santosh Panjikar
- Australian Synchrotron, 800 Blackburn
Road, Clayton, Victoria 3168, Australia
| | - Stephanie C. Pero
- Department
of Surgery and Vermont Cancer Center, University of Vermont, Burlington, Vermont 05401, United States
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