1
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Coricello A, Zhu W, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Takagi Y, Richards NGJ. Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase. bioRxiv 2023:2023.05.16.541009. [PMID: 37292727 PMCID: PMC10245805 DOI: 10.1101/2023.05.16.541009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
How dynamical motions in enzymes might be linked to catalytic function is of significant general interest, although almost all relevant experimental data, to date, has been obtained for enzymes with a single active site. Recent advances in X-ray crystallography and cryogenic electron microscopy offer the promise of elucidating dynamical motions for proteins that are not amenable to study using solution-phase NMR methods. Here we use 3D variability analysis (3DVA) of an EM structure for human asparagine synthetase (ASNS) in combination with atomistic molecular dynamics (MD) simulations to detail how dynamic motions of a single side chain mediates interconversion of the open and closed forms of a catalytically relevant intramolecular tunnel, thereby regulating catalytic function. Our 3DVA results are consistent with those obtained independently from MD simulations, which further suggest that formation of a key reaction intermediate acts to stabilize the open form of the tunnel in ASNS to permit ammonia translocation and asparagine formation. This conformational selection mechanism for regulating ammonia transfer in human ASNS contrasts sharply with those employed in other glutamine-dependent amidotransferases that possess a homologous glutaminase domain. Our work illustrates the power of cryo-EM to identify localized conformational changes and hence dissect the conformational landscape of large proteins. When combined with MD simulations, 3DVA is a powerful approach to understanding how conformational dynamics regulate function in metabolic enzymes with multiple active sites.
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Affiliation(s)
- Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", 61029 Urbino, Italy
| | - Wen Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- Present address: Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, 09042 Cagliari, Italy
| | - Carmen Gratteri
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Matthijn Vos
- NanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut Pasteur, 75015 Paris, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, 69367 Lyon, France
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
- NanoImaging Core Facility, Centre de Resources et Recherches Technologiques, Institut Pasteur, 75015 Paris, France
| | - Yuichiro Takagi
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
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2
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Richards NGJ, Bearne SL, Goto Y, Parker EJ. Reactivity and mechanism in chemical and synthetic biology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220023. [PMID: 36633278 PMCID: PMC9835593 DOI: 10.1098/rstb.2022.0023] [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: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 01/13/2023] Open
Abstract
Physical organic chemistry and mechanistic thinking provide a strong intellectual framework for understanding the chemical logic of evolvable informational macromolecules and metabolic transformations in living organisms. These concepts have also led to numerous successes in designing and applying tools to delineate biological function in health and disease, chemical ecology and possible alternative chemistries employed by extraterrestrial life. A symposium at the 2020 Pacifichem meeting was scheduled in December 2020 to discuss designing and exploiting expanded genetic alphabets, methods to understand the biosynthesis of natural products and re-engineering primary metabolism in bacteria. The COVID-19 pandemic led to postponement of in-person discussions, with the symposium eventually being held on 20-21 December 2021 as an online event. This issue is a written record of work presented on biosynthetic pathways and enzyme catalysis, engineering microorganisms with new metabolic capabilities, and the synthesis of non-canonical, nucleobases for medical applications and for studies of alternate chemistries for living organisms. The variety of opinion pieces, reviews and original research articles provide a starting point for innovations that clarify how complex biological systems emerge from the rules of chemical reactivity and mechanism. This article is part of the themed issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Foundation for Advanced Molecular Evolution, 13709 Progress Boulevard, Alachua, FL 32615, USA
| | - Stephen L. Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada B3H 4R2
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| | - Yuki Goto
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Emily J. Parker
- Department of Chemistry, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand
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3
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Li W, Girt GC, Radadiya A, Stewart JJP, Richards NGJ, Naismith JH. Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase. Open Biol 2023; 13:220287. [PMID: 36629016 PMCID: PMC9832568 DOI: 10.1098/rsob.220287] [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] [Indexed: 01/12/2023] Open
Abstract
The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1H-pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.
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Affiliation(s)
- Wenbo Li
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK,Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Georgina C. Girt
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | | | - Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK,Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK,Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, Oxford OX3 7BN, UK
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4
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Bijani S, Shaikh F, Mirza S, Weng In Siu S, Jain N, Rawal R, Richards NGJ, Shah A, Radadiya A. Novel Dihydropyrimidinone Derivatives as Potential P-Glycoprotein Modulators. ACS Omega 2022; 7:16278-16287. [PMID: 35601326 PMCID: PMC9118204 DOI: 10.1021/acsomega.1c05839] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/15/2022] [Indexed: 05/22/2023]
Abstract
P-glycoprotein (Pgp), an ATP binding cassette (ABC) transporter, is an ATP-dependent efflux pump responsible for cancer multidrug resistance. As part of efforts to identify human Pgp (hPgp) inhibitors, we prepared a series of novel triazole-conjugated dihydropyrimidinones using a synthetic approach that is well suited for obtaining compound libraries. Several of these dihydropyrimidinone derivatives modulate human P-glycoprotein (hPgp) activity with low micromolar EC50 values. Molecular docking studies suggest that these compounds bind to the M-site of the transporter.
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Affiliation(s)
- Sabera Bijani
- Center
of Excellence, National Facility for Drug Discovery Complex, Department
of Chemistry, Saurashtra University, Rajkot 360005, India
- Department
of Chemistry, Marwadi University, Rajkot 360003, India
| | - Faraz Shaikh
- Center
of Excellence, National Facility for Drug Discovery Complex, Department
of Chemistry, Saurashtra University, Rajkot 360005, India
- Department
of Computer and Information Science, University
of Macau, Macau 999078, China
| | - Sheefa Mirza
- The
Gujarat Cancer & Research Institute, Ahmedabad 380009, India
- Department
of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Shirley Weng In Siu
- Department
of Computer and Information Science, University
of Macau, Macau 999078, China
| | - Nayan Jain
- Department
of Life Sciences, School of Sciences, Gujarat
University, Ahmedabad 380009, India
| | - Rakesh Rawal
- The
Gujarat Cancer & Research Institute, Ahmedabad 380009, India
- Department
of Life Sciences, School of Sciences, Gujarat
University, Ahmedabad 380009, India
| | | | - Anamik Shah
- Center
of Excellence, National Facility for Drug Discovery Complex, Department
of Chemistry, Saurashtra University, Rajkot 360005, India
- Astha, Saurashtra
University Karmachari Cooperative Society,
B/H Forensic Lab., Street
No. 2, University Road, Rajkot 360005, India
| | - Ashish Radadiya
- Center
of Excellence, National Facility for Drug Discovery Complex, Department
of Chemistry, Saurashtra University, Rajkot 360005, India
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
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5
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Riegert AS, Narindoshvili T, Coricello A, Richards NGJ, Raushel FM. Correction to "Functional Characterization of Two PLP-Dependent Enzymes Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni". Biochemistry 2021; 61:46. [PMID: 34928582 DOI: 10.1021/acs.biochem.1c00789] [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: 11/29/2022]
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Riegert AS, Narindoshvili T, Coricello A, Richards NGJ, Raushel FM. Functional Characterization of Two PLP-Dependent Enzymes Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni. Biochemistry 2021; 60:2836-2843. [PMID: 34505775 DOI: 10.1021/acs.biochem.1c00439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a Gram-negative, pathogenic bacterium that causes campylobacteriosis, a form of gastroenteritis. C. jejuni is the most frequent cause of food-borne illness in the world, surpassing Salmonella and E. coli. Coating the surface of C. jejuni is a layer of sugar molecules known as the capsular polysaccharide that, in C. jejuni NCTC 11168, is composed of a repeating unit of d-glycero-l-gluco-heptose, d-glucuronic acid, d-N-acetyl-galactosamine, and d-ribose. The d-glucuronic acid moiety is further amidated with either serinol or ethanolamine. It is unknown how these modifications are synthesized and attached to the polysaccharide. Here, we report the catalytic activities of two previously uncharacterized, pyridoxal phosphate (PLP)-dependent enzymes, Cj1436 and Cj1437, from C. jejuni NCTC 11168. Using a combination of mass spectrometry and nuclear magnetic resonance, we determined that Cj1436 catalyzes the decarboxylation of l-serine phosphate to ethanolamine phosphate. Cj1437 was shown to catalyze the transamination of dihydroxyacetone phosphate to (S)-serinol phosphate in the presence of l-glutamate. The probable routes to the ultimate formation of the glucuronamide substructures in the capsular polysaccharides of C. jejuni are discussed.
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Affiliation(s)
- Alexander S Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Adriana Coricello
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better polymerases: Engineering the replication of expanded genetic alphabets. J Biol Chem 2020; 295:17046-17059. [PMID: 33004440 PMCID: PMC7863901 DOI: 10.1074/jbc.rev120.013745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
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Affiliation(s)
- Zahra Ouaray
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom; Foundation for Applied Molecular Evolution, Alachua, Florida, USA.
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8
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Abstract
l-Asparaginase (EC 3.5.1.1) was first used as a component of combination drug therapies to treat acute lymphoblastic leukemia (ALL), a cancer of the blood and bone marrow, almost 50 years ago. Administering this enzyme to reduce asparagine levels in the blood is a cornerstone of modern clinical protocols for ALL; indeed, this remains the only successful example of a therapy targeted against a specific metabolic weakness in any form of cancer. Three problems, however, constrain the clinical use of l-asparaginase. First, a type II bacterial variant of l-asparaginase is administered to patients, the majority of whom are children, which produces an immune response thereby limiting the time over which the enzyme can be tolerated. Second, l-asparaginase is subject to proteolytic degradation in the blood. Third, toxic side effects are observed, which may be correlated with the l-glutaminase activity of the enzyme. This Perspective will outline how asparagine depletion negatively impacts the growth of leukemic blasts, discuss the structure and mechanism of l-asparaginase, and briefly describe the clinical use of chemically modified forms of clinically useful l-asparaginases, such as Asparlas, which was recently given FDA approval for use in children (babies to young adults) as part of multidrug treatments for ALL. Finally, we review ongoing efforts to engineer l-asparaginase variants with improved therapeutic properties and briefly detail emerging, alternate strategies for the treatment of forms of ALL that are resistant to asparagine depletion.
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Affiliation(s)
- Ashish Radadiya
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Wen Zhu
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Adriana Coricello
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K.,Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy.,Net4Science, Università "Magna Græcia" di Catanzaro, 88100 Catanzaro, Italy
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, 13079 Progress Boulevard, Alachua, Florida 32615, United States
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9
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Gao S, Radadiya A, Li W, Liu H, Zhu W, de Crécy-Lagard V, Richards NGJ, Naismith JH. Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex. Chem Commun (Camb) 2020; 56:7617-7620. [PMID: 32515440 PMCID: PMC8183095 DOI: 10.1039/d0cc02834g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
The enzyme ForT catalyzes C-C bond formation between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of formycin A 5'-phosphate by Streptomyces kaniharaensis. We report the 2.5 Å resolution structure of the ForT/PRPP complex and locate active site residues critical for PRPP recognition and catalysis.
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Affiliation(s)
- Sisi Gao
- Research Complex at Harwell, Didcot, OX11 0FA, UK and BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Wenbo Li
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK.
| | - Huanting Liu
- BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Wen Zhu
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK. and The Rosalind Franklin Institute, Didcot, OX11 0FA, UK
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10
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Eberlein L, Beierlein FR, van Eikema Hommes NJR, Radadiya A, Heil J, Benner SA, Clark T, Kast SM, Richards NGJ. Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet. J Chem Theory Comput 2020; 16:2766-2777. [PMID: 32125859 DOI: 10.1021/acs.jctc.9b01079] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.
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Affiliation(s)
- Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Frank R Beierlein
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Nico J R van Eikema Hommes
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Timothy Clark
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
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11
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Ouaray Z, Singh I, Georgiadis MM, Richards NGJ. Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase. Protein Sci 2020; 29:455-468. [PMID: 31654473 PMCID: PMC6954703 DOI: 10.1002/pro.3762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/16/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 01/02/2023]
Abstract
Obtaining semisynthetic microorganisms that exploit the information density of "hachimoji" DNA requires access to engineered DNA polymerases. A KlenTaq variant has been reported that incorporates the "hachimoji" P:Z nucleobase pair with a similar efficiency to that seen for Watson-Crick nucleobase incorporation by the wild type (WT) KlenTaq DNA polymerase. The variant polymerase differs from WT KlenTaq by only four amino acid substitutions, none of which are located within the active site. We now report molecular dynamics (MD) simulations on a series of binary complexes aimed at elucidating the contributions of the four amino acid substitutions to altered catalytic activity. These simulations suggest that WT KlenTaq is insufficiently flexible to be able to bind AEGIS DNA correctly, leading to the loss of key protein/DNA interactions needed to position the binary complex for efficient incorporation of the "hachimoji" Z nucleobase. In addition, we test literature hypotheses about the functional roles of each amino acid substitution and provide a molecular description of how individual residue changes contribute to the improved activity of the KlenTaq variant. We demonstrate that MD simulations have a clear role to play in systematically screening DNA polymerase variants capable of incorporating different types of nonnatural nucleobases thereby limiting the number that need to be characterized by experiment. It is now possible to build DNA molecules containing nonnatural nucleobase pairs in addition to A:T and G:C. Exploiting this development in synthetic biology requires engineered DNA polymerases that can replicate nonnatural nucleobase pairs. Computational studies on a DNA polymerase variant reveal how amino acid substitutions outside of the active site yield an enzyme that replicates nonnatural nucleobase pairs with high efficiency. This work will facilitate efforts to obtain bacteria possessing an expanded genetic alphabet.
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Affiliation(s)
| | - Isha Singh
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndiana
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndiana
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12
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Zhu W, Radadiya A, Bisson C, Wenzel S, Nordin BE, Martínez-Márquez F, Imasaki T, Sedelnikova SE, Coricello A, Baumann P, Berry AH, Nomanbhoy TK, Kozarich JW, Jin Y, Rice DW, Takagi Y, Richards NGJ. Erratum: Author Correction: High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity. Commun Biol 2019; 2:438. [PMID: 31799439 PMCID: PMC6874536 DOI: 10.1038/s42003-019-0690-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen Zhu
- 1School of Chemistry, Cardiff University, Cardiff, UK.,10Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | | | - Claudine Bisson
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,10Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | - Sabine Wenzel
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Brian E Nordin
- 4ActivX Biosciences, Inc, La Jolla, CA USA.,Present Address: Vividion Therapeutics, San Diego, CA USA
| | - Francisco Martínez-Márquez
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Tsuyoshi Imasaki
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA.,5Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Svetlana E Sedelnikova
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Adriana Coricello
- 1School of Chemistry, Cardiff University, Cardiff, UK.,Dipartimento di Scienze della Salute "Magna Græcia" di Catanzaro, Viale Europa, 88100 Catanzaro, Italy.,7Net4Science academic spinoff, Università "Magna Græcia", Campus Salvatore Venuta, Viale Europa, 88100 Catanzaro, Italy
| | | | - Alexandria H Berry
- 8Department of Biology, California Institute of Technology, Pasadena, CA USA
| | | | | | - Yi Jin
- 1School of Chemistry, Cardiff University, Cardiff, UK
| | - David W Rice
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Yuichiro Takagi
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Nigel G J Richards
- 1School of Chemistry, Cardiff University, Cardiff, UK.,9Foundation for Applied Molecular Evolution, Alachua, FL USA
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13
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Gao S, Liu H, de Crécy-Lagard V, Zhu W, Richards NGJ, Naismith JH. PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis. Chem Commun (Camb) 2019; 55:14502-14505. [PMID: 31730149 PMCID: PMC6927412 DOI: 10.1039/c9cc06975e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 01/04/2023]
Abstract
ForI is a PLP-dependent enzyme from the biosynthetic pathway of the C-nucleoside antibiotic formycin. Cycloserine is thought to inhibit PLP-dependent enzymes by irreversibly forming a PMP-isoxazole. We now report that ForI forms novel PMP-diketopiperazine derivatives following incubation with both d and l cycloserine. This unexpected result suggests chemical diversity in the chemistry of cycloserine inhibition.
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Affiliation(s)
- Sisi Gao
- Research Complex at Harwell
,
Didcot
, OX11 0FA
, UK
- BSRC
, University of St Andrews
,
St Andrews
, KY16 9ST
, UK
| | - Huanting Liu
- BSRC
, University of St Andrews
,
St Andrews
, KY16 9ST
, UK
| | | | - Wen Zhu
- Department of Chemistry and California
, Institute for Quantitative Biosciences
, University of California
,
Berkeley
, CA 94720
, USA
| | - Nigel G. J. Richards
- School of Chemistry
, Cardiff University
, Park Place
,
Cardiff
, CF10 3AT
, UK
- Foundation for Applied Molecular Evolution
,
Alachua
, FL 32415
, USA
| | - James H. Naismith
- Division of Structural Biology
, University of Oxford
,
Oxford
, OX3 7BN
, UK
.
- The Rosalind Franklin Institute
,
Didcot
, OX11 0FA
, UK
- State Key Laboratory of Biotherapy
, University of Sichuan
,
China
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14
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Zhu W, Radadiya A, Bisson C, Wenzel S, Nordin BE, Martínez-Márquez F, Imasaki T, Sedelnikova SE, Coricello A, Baumann P, Berry AH, Nomanbhoy TK, Kozarich JW, Jin Y, Rice DW, Takagi Y, Richards NGJ. High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity. Commun Biol 2019; 2:345. [PMID: 31552298 PMCID: PMC6748925 DOI: 10.1038/s42003-019-0587-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 09/06/2018] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Expression of human asparagine synthetase (ASNS) promotes metastatic progression and tumor cell invasiveness in colorectal and breast cancer, presumably by altering cellular levels of L-asparagine. Human ASNS is therefore emerging as a bona fide drug target for cancer therapy. Here we show that a slow-onset, tight binding inhibitor, which exhibits nanomolar affinity for human ASNS in vitro, exhibits excellent selectivity at 10 μM concentration in HCT-116 cell lysates with almost no off-target binding. The high-resolution (1.85 Å) crystal structure of human ASNS has enabled us to identify a cluster of negatively charged side chains in the synthetase domain that plays a key role in inhibitor binding. Comparing this structure with those of evolutionarily related AMP-forming enzymes provides insights into intermolecular interactions that give rise to the observed binding selectivity. Our findings demonstrate the feasibility of developing second generation human ASNS inhibitors as lead compounds for the discovery of drugs against metastasis. Wen Zhu et al. report the crystal structure of human asparagine synthetase at a 1.85 Å resolution, enabling computational analysis of inhibitor binding. They also find new insights into the intermolecular interactions contributing to binding specificity of inhibitors.
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Affiliation(s)
- Wen Zhu
- 1School of Chemistry, Cardiff University, Cardiff, UK.,8Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | | | - Claudine Bisson
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,8Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | - Sabine Wenzel
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Brian E Nordin
- 4ActivX Biosciences, Inc, La Jolla, CA USA.,Present Address: Vividion Therapeutics, San Diego, CA USA
| | - Francisco Martínez-Márquez
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Tsuyoshi Imasaki
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA.,5Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Svetlana E Sedelnikova
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | | | - Alexandria H Berry
- 6Department of Biology, California Institute of Technology, Pasadena, CA USA
| | | | | | - Yi Jin
- 1School of Chemistry, Cardiff University, Cardiff, UK
| | - David W Rice
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Yuichiro Takagi
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Nigel G J Richards
- 1School of Chemistry, Cardiff University, Cardiff, UK.,7Foundation for Applied Molecular Evolution, Alachua, FL USA
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15
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Zhu W, Reinhardt LA, Richards NGJ. Second-Shell Hydrogen Bond Impacts Transition-State Structure in Bacillus subtilis Oxalate Decarboxylase. Biochemistry 2018; 57:3425-3432. [DOI: 10.1021/acs.biochem.8b00214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen Zhu
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Laurie A. Reinhardt
- Institute for Enzyme Research and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726, United States
| | - Nigel G. J. Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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16
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, 19 F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017; 56:9732-9735. [PMID: 28498638 PMCID: PMC5575484 DOI: 10.1002/anie.201703074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 11/08/2022]
Abstract
We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF3- , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O3G and thence to PG . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Robert W Molt
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,ENSCO, Inc., Melbourne, FL, 32940, USA
| | - Erika Pellegrini
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
| | - Matthew W Bowler
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France.,European Molecular Biology Laboratory, Grenoble Outstation CS90181, 38042, Grenoble, Cedex 9, France
| | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
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17
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Sheng X, Zhu W, Huddleston J, Xiang DF, Raushel FM, Richards NGJ, Himo F. A Combined Experimental-Theoretical Study of the LigW-Catalyzed Decarboxylation of 5-Carboxyvanillate in the Metabolic Pathway for Lignin Degradation. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01166] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiang Sheng
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Wen Zhu
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - Jamison Huddleston
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Fen Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | | | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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18
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Richards NGJ, Georgiadis MM. Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System. Acc Chem Res 2017; 50:1375-1382. [PMID: 28594167 DOI: 10.1021/acs.accounts.6b00655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although the fundamental properties of DNA as first proposed by Watson and Crick in 1953 provided a basic understanding of how duplex DNA was organized and might be replicated, it was not until the first crystal structures of DNA (Z-DNA in 1979, B-DNA in 1980, and A-DNA in 1982) that the true complexity of the molecule began to be appreciated. Many crystal structures of oligonucleotides have since shed light on the helical forms that "Watson-Crick" DNA can adopt, their associated groove widths, and the properties of the nucleobase pairs and their interactions in all three helical forms. Additional understanding of the properties of Watson-Crick DNA has been provided by computational studies employing a variety of theoretical methods. Together with these studies devoted to understanding Watson-Crick DNA, recent efforts to expand the genetic alphabet have founded a new field in synthetic biology. One of these efforts, the artificially expanded genetic information system (AEGIS) developed by Steven Benner and co-workers, takes advantage of orthogonal hydrogen bonding to produce DNA comprised of six nucleobase pairs, of which the most extensively studied is referred to as P:Z with P being 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) and Z being 6-amino-5-nitro-2(1H)-pyridone. P:Z forms three edge-on hydrogen bonds that differ from standard Watson-Crick pairs in the arrangement of acceptors and donor groups; P presents acceptor, acceptor, donor, and Z presents donor, donor, acceptor. Z is unique among the AEGIS nucleobases in having a nitro group present in the major groove. PZ-containing DNA has been exploited in a number of clinical applications and is being used to develop receptors and catalysts. Ultimately, the grand challenge will be to create a semisynthetic organism with an expanded genome. Furthermore, just as our understanding of the properties of natural DNA have benefited from structural and computational characterization, so too will our understanding of artificial DNA. This Account focuses on the structural and biophysical properties of AEGIS DNA containing P:Z pairs. We begin with the fundamental properties of P:Z nucleobase pairs, including their electrostatic potential and hydrogen-bonding energies, as elucidated by quantum mechanical calculations. We then examine the impact of including multiple consecutive P:Z pairs into duplex DNA providing an opportunity to investigate stacking interactions between P:Z pairs. The self-complementary 5'-CTTATPPTAZZATAAG was crystallized in B-form using the host-guest system along with analogous natural sequences including Gs or As. Use of the host-guest system to characterize B-DNA obviates a number of limitations on the structural characterization of sequences of interest; these include the ability to crystallize the desired sequences and to distinguish structural effects imparted by the lattice constraints from those inherent in the sequence itself. On the other hand, 3/6ZP, 5'-CTTATPPPZZZATAAG, was crystallized in A-form in a DNA-only lattice allowing a comparative analysis of P:Z pairs in two of the biologically relevant helical forms: A- and B-DNA. Computational studies on the 3/6ZP sequence starting in A-form provide additional evidence for a more energetically favorable stacking interaction, which we term the "slide" conformer, observed in the A-form crystal structure; this unusual stacking interaction plays a major role in altering the conformational dynamics observed for the PZ-containing duplex as compared to a GC-containing "control" duplex in long time scale molecular dynamics simulations. This combined use of structural and computational strategies paves the way for obtaining a detailed description of artificial DNA, both in how it differs from Watson-Crick DNA and in the rational discovery of proteins, such as endonucleases, transcription factors, and polymerases, which can specifically manipulate DNA containing AEGIS nucleobase pairs.
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Affiliation(s)
- Nigel G. J. Richards
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Alachua, Florida 32615, United States
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department
of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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19
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography,
19
F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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)
- Yi Jin
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- School of ChemistryCardiff University Cardiff CF10 3AT UK
| | - Robert W. Molt
- School of ChemistryCardiff University Cardiff CF10 3AT UK
- Department of Biochemistry and Molecular BiologyIndiana University School of Medicine Indianapolis IN 46202 USA
- ENSCO, Inc. Melbourne FL 32940 USA
| | - Erika Pellegrini
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
| | | | - Matthew W. Bowler
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
- European Molecular Biology Laboratory, Grenoble Outstation CS90181 38042 Grenoble, Cedex 9 France
| | | | - G. Michael Blackburn
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- Manchester Institute of Biotechnology Manchester M1 7DN UK
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20
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Blackburn GM, Cherfils J, Moss GP, Richards NGJ, Waltho JP, Williams NH, Wittinghofer A. How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016). PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0202] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractProcedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to “best practice” in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.
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Affiliation(s)
- G. Michael Blackburn
- 1Department of Molecular Biology, Krebs Institute, University of Sheffield, S10 2TN, UK
| | - Jacqueline Cherfils
- 2Laboratoire de Biologie et Pharmacologie Appliquée, CNRS – École Normale Supérieure Paris-Saclay, Cachan, France. http://orcid.org/0000-0002-8966-3067
| | - Gerard P. Moss
- 3Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, UK
| | - Nigel G. J. Richards
- 4Department of Chemistry, Indiana University Purdue University Indianapolis, IL 46202, USA; and School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | | | | | - Alfred Wittinghofer
- 7Group for Structural Biology, Max-Planck-Institut für Molekulare Physiologie, 44227 Dortmund, Deutschland
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21
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Sharma PK, Balwani S, Mathur D, Malhotra S, Singh BK, Prasad AK, Len C, Van der Eycken EV, Ghosh B, Richards NGJ, Parmar VS. Synthesis and anti-inflammatory activity evaluation of novel triazolyl-isatin hybrids. J Enzyme Inhib Med Chem 2016; 31:1520-6. [PMID: 27146339 DOI: 10.3109/14756366.2016.1151015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
New isatin-triazole based hybrids have been synthesized and evaluated for their inhibitory activity of TNF-α induced expression of Intercellular Adhesion Molecule-1 (ICAM-1) on the surface of human endothelial cells. Structure-activity relationship (SAR) studies revealed that the presence of the electron-attracting bromo substituent at position-5 of the isatin moiety played an important role in enhancing the anti-inflammatory potential of the synthesized compounds. Z-1-[3-(1H-1,2,4-Triazol-1-yl)propyl]-5-bromo-3-[2-(4-methoxyphenyl)hydrazono]indolin-2-one (19) with an IC50 = 20 μM and 89% ICAM-1 inhibition with MTD at 200 μM was found to be the most potent of all the synthesized derivatives. Introduction of 1,2,4-triazole ring and electron-donating methoxy group on the phenylhydrazone moiety resulted in four-fold increase of the anti-inflammatory activity.
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Affiliation(s)
- Pramod K Sharma
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India .,b Chemical Research Laboratory, Wockhardt Research Centre , Aurangabad , Maharashtra , India
| | - Sakshi Balwani
- c Immunogenetics Laboratory, CSIR-Institute of Genomics and Integrative Biology , Delhi , India
| | - Divya Mathur
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India .,d Department of Chemistry , Daulat Ram College, University of Delhi , Delhi , India
| | - Shashwat Malhotra
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Brajendra K Singh
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Ashok K Prasad
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India
| | - Christophe Len
- e Sorbonne Universités, Université de Technologie de Compiègne (UTC), Ecole Supérieure de Chimie Organique et Minérale (ESCOM) , Compiègne Cedex , France .,f Department of Chemistry , University of Hull , Hull , UK
| | - Erik V Van der Eycken
- g Department of Chemistry , Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), University of Leuven (KU Leuven) , Leuven , Belgium
| | - Balaram Ghosh
- c Immunogenetics Laboratory, CSIR-Institute of Genomics and Integrative Biology , Delhi , India
| | - Nigel G J Richards
- h Department of Chemistry and Chemical Biology , Indiana University-Purdue University (IUPUI) , Indianapolis , IN , USA , and.,i School of Chemistry, College of Physical Sciences & Engineering, Cardiff University , Cardiff , UK
| | - Virinder S Parmar
- a Department of Chemistry , Bioorganic Laboratory, University of Delhi , Delhi , India .,e Sorbonne Universités, Université de Technologie de Compiègne (UTC), Ecole Supérieure de Chimie Organique et Minérale (ESCOM) , Compiègne Cedex , France .,h Department of Chemistry and Chemical Biology , Indiana University-Purdue University (IUPUI) , Indianapolis , IN , USA , and
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22
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Zhu W, Easthon LM, Reinhardt LA, Tu C, Cohen SE, Silverman DN, Allen KN, Richards NGJ. Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase. Biochemistry 2016; 55:2163-73. [PMID: 27014926 PMCID: PMC4854488 DOI: 10.1021/acs.biochem.6b00043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Oxalate
decarboxylase (OxDC) catalyzes the conversion of oxalate
into formate and carbon dioxide in a remarkable reaction that requires
manganese and dioxygen. Previous studies have shown that replacing
an active-site loop segment Ser161-Glu162-Asn163-Ser164 in the N-terminal domain of OxDC with
the cognate residues Asp161-Ala162-Ser-163-Asn164 of an evolutionarily related, Mn-dependent
oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly
increased oxidase activity. The mechanistic basis for this change
in activity has now been investigated using membrane inlet mass spectrometry
(MIMS) and isotope effect (IE) measurements. Quantitative analysis
of the reaction stoichiometry as a function of oxalate concentration,
as determined by MIMS, suggests that the increased oxidase activity
of the DASN OxDC variant is associated with only a small fraction
of the enzyme molecules in solution. In addition, IE measurements
show that C–C bond cleavage in the DASN OxDC variant proceeds
via the same mechanism as in the wild-type enzyme, even though the
Glu162 side chain is absent. Thus, replacement of the loop
residues does not modulate the chemistry of the enzyme-bound Mn(II)
ion. Taken together, these results raise the possibility that the
observed oxidase activity of the DASN OxDC variant arises from an
increased level of access of the solvent to the active site during
catalysis, implying that the functional role of Glu162 is
to control loop conformation. A 2.6 Å resolution X-ray crystal
structure of a complex between oxalate and the Co(II)-substituted
ΔE162 OxDC variant, in which Glu162 has been deleted
from the active site loop, reveals the likely mode by which the substrate
coordinates the catalytically active Mn ion prior to C–C bond
cleavage. The “end-on” conformation of oxalate observed
in the structure is consistent with the previously published V/K IE data and provides an empty coordination
site for the dioxygen ligand that is thought to mediate the formation
of Mn(III) for catalysis upon substrate binding.
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Affiliation(s)
- Wen Zhu
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
| | - Lindsey M Easthon
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - Laurie A Reinhardt
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53726, United States
| | - Chingkuang Tu
- Department of Pharmacology & Therapeutics, University of Florida , Gainesville, Florida 32610, United States
| | - Steven E Cohen
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - David N Silverman
- Department of Pharmacology & Therapeutics, University of Florida , Gainesville, Florida 32610, United States
| | - Karen N Allen
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - Nigel G J Richards
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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23
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. (19)F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016; 55:3318-22. [PMID: 26822702 PMCID: PMC4770445 DOI: 10.1002/anie.201509477] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/14/2016] [Indexed: 11/13/2022]
Abstract
Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use (19)F NMR chemical shifts in the MgF3(-) transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3(-) oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3(-) group based on the structure of a RhoA/GAP-GDP-MgF3(-) TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85' side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln-63 carboxamide by Arg85' to preclude direct hydrogen bonding from water to the target γ-PO3(-) group.
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Affiliation(s)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert W Molt
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jonathan P Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK.
| | - Nigel G J Richards
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
| | - G Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
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24
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. 19F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509477] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
| | - Robert W. Molt
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - Jonathan P. Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
- Manchester Institute of Biotechnology; Manchester M1 7DN UK
| | - Nigel G. J. Richards
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
- School of Chemistry; Cardiff University; Cardiff CF10 3AT UK
| | - G. Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
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25
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Vladimirova A, Patskovsky Y, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Hillerich B, Seidel RD, Richards NGJ, Almo SC, Raushel FM. Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase. J Am Chem Soc 2016; 138:826-36. [PMID: 26714575 PMCID: PMC4732527 DOI: 10.1021/jacs.5b08251] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
5-Carboxyvanillate
decarboxylase (LigW) catalyzes the conversion
of 5-carboxyvanillate to vanillate in the biochemical pathway for
the degradation of lignin. This enzyme was shown to require Mn2+ for catalytic activity and the kinetic constants for the
decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s–1 and kcat/Km = 4.0 × 104 M–1 s–1) and Novosphingobium aromaticivorans (kcat = 27 s–1 and kcat/Km = 1.1 × 105 M–1 s–1) were determined. The three-dimensional structures of both enzymes
were determined in the presence and absence of ligands bound in the
active site. The structure of LigW from N. aromaticivorans, bound with the substrate analogue, 5-nitrovanillate (Kd = 5.0 nM), was determined to a resolution of 1.07 Å.
The structure of this complex shows a remarkable enzyme-induced distortion
of the nitro-substituent out of the plane of the phenyl ring by approximately
23°. A chemical reaction mechanism for the decarboxylation of
5-carboxyvanillate by LigW was proposed on the basis of the high resolution
X-ray structures determined in the presence ligands bound in the active
site, mutation of active site residues, and the magnitude of the product
isotope effect determined in a mixture of H2O and D2O. In the proposed reaction mechanism the enzyme facilitates
the transfer of a proton to C5 of the substrate prior to the decarboxylation
step.
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Affiliation(s)
- Anna Vladimirova
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Yury Patskovsky
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Alexander A Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Elena V Fedorov
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Rafael Toro
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Brandan Hillerich
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Ronald D Seidel
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Nigel G J Richards
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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26
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Zhu W, Wilcoxen J, Britt RD, Richards NGJ. Formation of Hexacoordinate Mn(III) in Bacillus subtilis Oxalate Decarboxylase Requires Catalytic Turnover. Biochemistry 2016; 55:429-34. [PMID: 26744902 DOI: 10.1021/acs.biochem.5b01340] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oxalate decarboxylase (OxDC) catalyzes the disproportionation of oxalic acid monoanion into CO2 and formate. The enzyme has long been hypothesized to utilize dioxygen to form mononuclear Mn(III) or Mn(IV) in the catalytic site during turnover. Recombinant OxDC, however, contains only tightly bound Mn(II), and direct spectroscopic detection of the metal in higher oxidation states under optimal catalytic conditions (pH 4.2) has not yet been reported. Using parallel mode electron paramagnetic resonance spectroscopy, we now show that substantial amounts of Mn(III) are indeed formed in OxDC, but only in the presence of oxalate and dioxygen under acidic conditions. These observations provide the first direct support for proposals in which Mn(III) removes an electron from the substrate to yield a radical intermediate in which the barrier to C-C bond cleavage is significantly decreased. Thus, OxDC joins a small list of enzymes capable of stabilizing and controlling the reactivity of the powerful oxidizing species Mn(III).
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Affiliation(s)
- Wen Zhu
- Department of Chemistry & Chemical Biology, Indiana University Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
| | - Jarett Wilcoxen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Nigel G J Richards
- Department of Chemistry & Chemical Biology, Indiana University Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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27
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Kumar A, Khan A, Malhotra S, Mosurkal R, Dhawan A, Pandey MK, Singh BK, Kumar R, Prasad AK, Sharma SK, Samuelson LA, Cholli AL, Len C, Richards NGJ, Kumar J, Haag R, Watterson AC, Parmar VS. Synthesis of macromolecular systems via lipase catalyzed biocatalytic reactions: applications and future perspectives. Chem Soc Rev 2016; 45:6855-6887. [DOI: 10.1039/c6cs00147e] [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] [Indexed: 01/10/2023]
Abstract
This review highlights the application of lipases in the synthesis of pharmaceutically important small molecules and polymers for diverse applications.
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28
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Molt RW, Watson T, Bazanté AP, Bartlett RJ, Richards NGJ. Gas phase RDX decomposition pathways using coupled cluster theory. Phys Chem Chem Phys 2016; 18:26069-26077. [DOI: 10.1039/c6cp05121a] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic and free energy barriers for a series of gas-phase RDX decomposition mechanisms have been obtain using coupled cluster singles, doubles, and perturbative triples with complete basis set (CCSD(T)/CBS) electronic energies for MBPT(2)/cc-pVTZ structures.
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Affiliation(s)
- Robert W. Molt
- Department of Chemistry and Chemical Biology
- Indiana University-Purdue University Indianapolis
- Indianapolis
- USA
- School of Chemistry
| | - Thomas Watson
- Quantum Theory Project
- University of Florida
- Gainesville
- USA
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29
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Chang CH, Richards NGJ. Intrinsic Carbon-Carbon Bond Reactivity at the Manganese Center of Oxalate Decarboxylase from Density Functional Theory. J Chem Theory Comput 2015; 1:994-1007. [PMID: 26641915 DOI: 10.1021/ct050063d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The detailed manganese-dependent chemistry employed by oxalate decarboxylase (OxDC) to catalyze the nonoxidative decarboxylation of oxalic acid remains poorly understood. For example, enzyme activity requires the presence of dioxygen even though this compound is not a formal substrate in the reaction. We now report density functional theory (DFT) calculations upon a series of hypothetical OxDC active site model structures. Our results suggest that the function of the metal ion may be to position dioxygen and oxalate such that electrons can be shuttled directly between these species, thereby removing the need for the existence of Mn(III) as an intermediate in the mechanism. These calculations also indicate that the intrinsic, gas-phase reactivity of the Bacillus subtilis oxalate decarboxylase active center is to oxidize oxalate. Since this reactivity is not observed for OxDC, our DFT results suggest that protein environment modulates the intrinsic metallocenter reactivity, presumably by affecting the electronic distribution at the manganese center during catalysis.
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Affiliation(s)
- Christopher H Chang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Nigel G J Richards
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
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30
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Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NGJ. Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc 2015; 137:6947-55. [PMID: 25961938 DOI: 10.1021/jacs.5b03482] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.
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31
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Abstract
Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution. Our results show that the calculated solution-phase free-energy barrier for C-C bond cleavage to form CO2 is decreased from 34.2 kcal/mol for oxalic acid to only 9.3 kcal/mol and a maximum of 3.5 kcal/mol for the cationic and neutral oxalic acid-derived radicals, respectively. These studies also show that the C-C σ bonding orbital of the radical cation contains only a single electron, giving rise to an elongated C-C bond distance of 1.7 Å; a similar lengthening of the C-C bond is not observed for the neutral radical. This study provides new chemical insights into the structure and stability of plausible intermediates in the catalytic mechanism of OxDC, and suggests that removal of an electron to form a radical (with or without the concomitant loss of a proton) may be a general strategy for cleaving the unreactive C-C bonds between adjacent sp(2)-hybridized carbon atoms.
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Affiliation(s)
- Robert W Molt
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University , Indianapolis, Indiana 46202, United States
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32
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Twahir UT, Stedwell CN, Lee CT, Richards NGJ, Polfer NC, Angerhofer A. Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4. Free Radic Biol Med 2015; 80:59-66. [PMID: 25526893 PMCID: PMC4355160 DOI: 10.1016/j.freeradbiomed.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 01/02/2023]
Abstract
This contribution describes the trapping of the hydroperoxyl radical at a pH of 4 during turnover of wild-type oxalate decarboxylase and its T165V mutant using the spin-trap BMPO. Radicals were detected and identified by a combination of EPR and mass spectrometry. Superoxide, or its conjugate acid, the hydroperoxyl radical, is expected as an intermediate in the decarboxylation and oxidation reactions of the oxalate monoanion, both of which are promoted by oxalate decarboxylase. Another intermediate, the carbon dioxide radical anion was also observed. The quantitative yields of superoxide trapping are similar in the wild type and the mutant while it is significantly different for the trapping of the carbon dioxide radical anion. This suggests that the two radicals are released from different sites of the protein.
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Affiliation(s)
- Umar T Twahir
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Cory T Lee
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Nigel G J Richards
- Department of Chemistry & Chemical Biology, Indiana University Purdue University, Indianapolis, Indianapolis, IN 46202, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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33
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Abstract
B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
| | - Whitney
F. Kellett
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Nigel G. J. Richards
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
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34
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Campomanes P, Kellett WF, Easthon LM, Ozarowski A, Allen KN, Angerhofer A, Rothlisberger U, Richards NGJ. Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations. J Am Chem Soc 2014; 136:2313-23. [PMID: 24444454 PMCID: PMC4004257 DOI: 10.1021/ja408138f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals associated with the two Mn(II) centers located in the N- and C-terminal cupin domains of the enzyme. We now report a mutational strategy that has established the assignment of EPR fine structure parameters to each of these Mn(II) centers at pH 8.5. These experimental findings are also used to assess the performance of a multistep strategy for calculating the zero-field splitting parameters of protein-bound Mn(II) ions. Despite the known sensitivity of calculated D and E values to the computational approach, we demonstrate that good estimates of these parameters can be obtained using cluster models taken from carefully optimized DFT/MM structures. Overall, our results provide new insights into the strengths and limitations of theoretical methods for understanding electronic properties of protein-bound Mn(II) ions, thereby setting the stage for future EPR studies on the electronic properties of the Mn(II) centers in OxDC and site-specific variants.
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Affiliation(s)
- Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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35
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Abstract
A novel rhodium–catalyzed imination of sulfoxides using O-(2,4-dinitrophenyl)hydroxylamine is developed under mild conditions with good functional group tolerance.
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Affiliation(s)
- Jinmin Miao
- Department of Chemistry and Chemical Biology Indiana University Purdue University Indianapolis
- Indianapolis, USA
| | - Nigel G. J. Richards
- Department of Chemistry and Chemical Biology Indiana University Purdue University Indianapolis
- Indianapolis, USA
| | - Haibo Ge
- Department of Chemistry and Chemical Biology Indiana University Purdue University Indianapolis
- Indianapolis, USA
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36
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Kellett WF, Brunk E, Desai BJ, Fedorov AA, Almo SC, Gerlt JA, Rothlisberger U, Richards NGJ. Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase. Biochemistry 2013; 52:1842-4. [PMID: 23452154 PMCID: PMC3788570 DOI: 10.1021/bi400093y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fermentation-respiration switch (FrsA) protein in Vibrio vulnificus was recently reported to catalyze the cofactor-independent decarboxylation of pyruvate. We now report quantum mechanical/molecular mechenical calculations that examine the energetics of C-C bond cleavage for a pyruvate molecule bound within the putative active site of FrsA. These calculations suggest that the barrier to C-C bond cleavage in the bound substrate is 28 kcal/mol, which is similar to that estimated for the uncatalyzed decarboxylation of pyruvate in water at 25 °C. In agreement with the theoretical predictions, no pyruvate decarboxylase activity was detected for recombinant FrsA protein that could be crystallized and structurally characterized. These results suggest that the functional annotation of FrsA as a cofactor-independent pyruvate decarboxylase is incorrect.
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Affiliation(s)
- Whitney F. Kellett
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
| | - Elizabeth Brunk
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Bijoy J. Desai
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| | - John A. Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
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37
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Ikeuchi H, Ahn YM, Otokawa T, Watanabe B, Hegazy L, Hiratake J, Richards NGJ. A sulfoximine-based inhibitor of human asparagine synthetase kills L-asparaginase-resistant leukemia cells. Bioorg Med Chem 2012; 20:5915-27. [PMID: 22951255 DOI: 10.1016/j.bmc.2012.07.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/19/2012] [Accepted: 07/24/2012] [Indexed: 11/27/2022]
Abstract
An adenylated sulfoximine transition-state analogue 1, which inhibits human asparagine synthetase (hASNS) with nanomolar potency, has been reported to suppress the proliferation of an l-asparagine amidohydrolase (ASNase)-resistant MOLT-4 leukemia cell line (MOLT-4R) when l-asparagine is depleted in the medium. We now report the synthesis and biological activity of two new sulfoximine analogues of 1 that have been studied as part of systematic efforts to identify compounds with improved cell permeability and/or metabolic stability. One of these new analogues, an amino sulfoximine 5 having no net charge at cellular pH, is a better hASNS inhibitor (K(I)(∗)=8 nM) than 1 and suppresses proliferation of MOLT-4R cells at 10-fold lower concentration (IC(50)=0.1mM). More importantly, and in contrast to the lead compound 1, the presence of sulfoximine 5 at concentrations above 0.25 mM causes the death of MOLT-4R cells even when ASNase is absent in the culture medium. The amino sulfoximine 5 exhibits different dose-response behavior when incubated with an ASNase-sensitive MOLT-4 cell line (MOLT-4S), supporting the hypothesis that sulfoximine 5 exerts its effect by inhibiting hASNS in the cell. Our work provides further evidence for the idea that hASNS represents a chemotherapeutic target for the treatment of leukemia, and perhaps other cancers, including those of the prostate.
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Affiliation(s)
- Hideyuki Ikeuchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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38
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Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NGJ. A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase. Biochemistry 2012; 51:2911-20. [PMID: 22404040 PMCID: PMC3319475 DOI: 10.1021/bi300001q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.
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Affiliation(s)
| | | | - Zhibing Lu
- Department of Chemistry, Boston University, Boston, MA 02215
| | - Mithila S. Shukla
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Linda Nguyen
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - W. Wallace Cleland
- Institute for Enzyme Research, University of Wisconsin, Madison, WI 53706
| | | | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215
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39
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Moral MEG, Tu C, Richards NGJ, Silverman DN. Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases. Anal Biochem 2011; 418:73-7. [PMID: 21782782 DOI: 10.1016/j.ab.2011.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 05/17/2011] [Accepted: 06/23/2011] [Indexed: 01/20/2023]
Abstract
Membrane inlet mass spectrometry (MIMS) uses diffusion across a permeable membrane to detect in solution uncharged molecules of small molecular weight. We point out here the application of MIMS to determine catalytic properties of decarboxylases using as an example catalysis by oxalate decarboxylase (OxDC) from Bacillus subtilis. The decarboxylase activity generates carbon dioxide and formate from the nonoxidative reaction but is accompanied by a concomitant oxidase activity that consumes oxalate and oxygen and generates CO(2) and hydrogen peroxide. The application of MIMS in measuring catalysis by OxDC involves the real-time and continuous detection of oxygen and product CO(2) from the ion currents of their respective mass peaks. Steady-state catalytic constants for the decarboxylase activity obtained by measuring product CO(2) using MIMS are comparable to those acquired by the traditional endpoint assay based on the coupled reaction with formate dehydrogenase, and measuring consumption of O(2) using MIMS also estimates the oxidase activity. The use of isotope-labeled substrate ((13)C(2)-enriched oxalate) in MIMS provides a method to characterize the catalytic reaction in cell suspensions by detecting the mass peak for product (13)CO(2) (m/z 45), avoiding inaccuracies due to endogenous (12)CO(2).
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Affiliation(s)
- Mario E G Moral
- Department of Chemistry, University of Florida, Gainesville, FL 32610, USA
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Moussatche P, Angerhofer A, Imaram W, Hoffer E, Uberto K, Brooks C, Bruce C, Sledge D, Richards NGJ, Moomaw EW. Characterization of Ceriporiopsis subvermispora bicupin oxalate oxidase expressed in Pichia pastoris. Arch Biochem Biophys 2011; 509:100-7. [PMID: 21376010 PMCID: PMC3078958 DOI: 10.1016/j.abb.2011.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/23/2011] [Accepted: 02/24/2011] [Indexed: 01/16/2023]
Abstract
Oxalate oxidase (E.C. 1.2.3.4) catalyzes the oxygen-dependent oxidation of oxalate to carbon dioxide in a reaction that is coupled with the formation of hydrogen peroxide. Although there is currently no structural information available for oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx), sequence data and homology modeling indicate that it is the first manganese-containing bicupin enzyme identified that catalyzes this reaction. Interestingly, CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC). We show that CsOxOx activity directly correlates with Mn content and other metals do not appear to be able to support catalysis. EPR spectra indicate that the Mn is present as Mn(II), and are consistent with the coordination environment expected from homology modeling with known X-ray crystal structures of OxDC from Bacillus subtilis. EPR spin-trapping experiments support the existence of an oxalate-derived radical species formed during turnover. Acetate and a number of other small molecule carboxylic acids are competitive inhibitors for oxalate in the CsOxOx catalyzed reaction. The pH dependence of this reaction suggests that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated.
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Affiliation(s)
- Patricia Moussatche
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Witcha Imaram
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Eric Hoffer
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Kelsey Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Christopher Brooks
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Crystal Bruce
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Daniel Sledge
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Ellen W. Moomaw
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
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Imaram W, Saylor BT, Centonze CP, Richards NGJ, Angerhofer A. EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction. Free Radic Biol Med 2011; 50:1009-15. [PMID: 21277974 PMCID: PMC3070241 DOI: 10.1016/j.freeradbiomed.2011.01.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 01/01/2011] [Accepted: 01/17/2011] [Indexed: 01/15/2023]
Abstract
EPR spin trapping experiments on bacterial oxalate decarboxylase from Bacillus subtilis under turn-over conditions are described. The use of doubly (13)C-labeled oxalate leads to a characteristic splitting of the observed radical adducts using the spin trap N-tert-butyl-α-phenylnitrone linking them directly to the substrate. The radical was identified as the carbon dioxide radical anion which is a key intermediate in the hypothetical reaction mechanism of both decarboxylase and oxidase activities. X-ray crystallography had identified a flexible loop, SENS161-4, which acts as a lid to the putative active site. Site directed mutagenesis of the hinge amino acids, S161 and T165 was explored and showed increased radical trapping yields compared to the wild type. In particular, T165V shows approximately ten times higher radical yields while at the same time its decarboxylase activity was reduced by about a factor of ten. This mutant lacks a critical H-bond between T165 and R92 resulting in compromised control over its radical chemistry allowing the radical intermediate to leak into the surrounding solution.
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Moral MEG, Tu C, Imaram W, Angerhofer A, Silverman DN, Richards NGJ. Nitric oxide reversibly inhibits Bacillus subtilis oxalate decarboxylase. Chem Commun (Camb) 2011; 47:3111-3. [PMID: 21264418 DOI: 10.1039/c0cc04946h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Membrane inlet mass spectrometry (MIMS) has been employed to assay the catalytic activity of oxalate decarboxylase (OxDC), allowing us to demonstrate that nitric oxide (NO) reversibly inhibits the enzyme under dioxygen-depleted conditions. X-band EPR measurements do not provide any direct evidence for the interaction of NO with either of the Mn(II) centers in OxDC raising the possibility that there is a separate dioxygen-binding pocket in the enzyme.
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Affiliation(s)
- Mario E G Moral
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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Chojnacka K, Santoro S, Awartani R, Richards NGJ, Himo F, Aponick A. Synthetic studies on the solanacol ABC ring system by cation-initiated cascade cyclization: implications for strigolactone biosynthesis. Org Biomol Chem 2011; 9:5350-3. [DOI: 10.1039/c1ob05751k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Meyer ME, Gutierrez JA, Raushel FM, Richards NGJ. A conserved glutamate controls the commitment to acyl-adenylate formation in asparagine synthetase. Biochemistry 2010; 49:9391-401. [PMID: 20853825 PMCID: PMC2975022 DOI: 10.1021/bi1010688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inhibitor docking studies have implicated a conserved glutamate residue (Glu-348) as a general base in the synthetase active site of the enzyme asparagine synthetase B from Escherichia coli (AS-B). We now report steady-state kinetic, isotope transfer, and positional isotope exchange experiments for a series of site-directed AS-B mutants in which Glu-348 is substituted by conservative amino acid replacements. We find that formation of the β-aspartyl-AMP intermediate, and therefore the eventual production of asparagine, is dependent on the presence of a carboxylate side chain at this position in the synthetase active site. In addition, Glu-348 may also play a role in mediating the conformational changes needed to (i) coordinate, albeit weakly, the glutaminase and synthetase activities of the enzyme and (ii) establish the structural integrity of the intramolecular tunnel along which ammonia is translocated. The importance of Glu-348 in mediating acyl-adenylate formation contrasts with the functional role of the cognate residues in β-lactam synthetase (BLS) and carbapenem synthetase (CPS) (Tyr-348 and Tyr-345, respectively), which both likely evolved from asparagine synthetase. Given the similarity of the chemistry catalyzed by AS-B, BLS, and CPS, our work highlights the difficulty of predicting the functional outcome of single site mutations on enzymes that catalyze almost identical chemical transformations.
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Affiliation(s)
- Megan E. Meyer
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
| | - Jemy A. Gutierrez
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, TX 77843
| | - Nigel G. J. Richards
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611
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45
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Lee S, Chen M, Yang W, Richards NGJ. Sampling long time scale protein motions: OSRW simulation of active site loop conformational free energies in formyl-CoA:oxalate CoA transferase. J Am Chem Soc 2010; 132:7252-3. [PMID: 20446682 PMCID: PMC2877758 DOI: 10.1021/ja101446u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray crystallographic snapshots have shown that conformational changes of a tetraglycine loop in the active site of formyl-CoA:oxalate CoA transferase (FRC) play an important role in the catalytic cycle of the enzyme. Orthogonal space random walk (OSRW) simulations have been applied to obtain quantitative computational estimates of the relative free energy of the "open" and "closed" conformations of this loop together with the energetic barrier for interconversion of these states in wild type FRC. These OSRW calculations not only show that the two conformations have similar free energies but also predict a barrier that is consistent with the observed turnover number of the enzyme. In an effort to quantitate the importance of specific residues in the tetraglycine loop, OSRW simulations have also been performed on the G258A, G259A, G260A, and G261A FRC variants both to examine the energetic effects of replacing each glycine residue and to correlate the computed energies with kinetic and structural observations. In enzymes with substantially reduced catalytic efficiency (k(cat)/K(M)), the OSRW simulations reveal the adoption of additional low energy loop conformations. In the case of the G260A FRC variant, the new conformation identified by simulation is similar to that observed in the X-ray crystal structure of the protein. These results provide further evidence for the power of the OSRW method in sampling conformational space and, hence, in providing quantitative free energy estimates for the conformations adopted by functionally important active site loops. In addition, these simulations model the motions of side chains that are correlated with changes in loop conformation thereby permitting access to long time-scale motions through the use of nanosecond simulations.
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Affiliation(s)
- Sangbae Lee
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Mengen Chen
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Wei Yang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
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Wang XS, Roitberg AE, Richards NGJ. Computational Studies of Ammonia Channel Function in Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase. Biochemistry 2009; 48:12272-82. [DOI: 10.1021/bi901521d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiang S. Wang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
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Abstract
Bacillus subtilis oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into CO(2) and formate. The enzyme is composed of two cupin domains, each of which contains a Mn(II) ion. Although there is general agreement that Mn(II) in the N-terminal domain mediates OxDC-catalyzed decarboxylation, legitimate questions have been raised concerning the function (if any) of the Mn(II) bound in the C-terminal cupin domain. We have investigated this problem using a series of OxDC mutants in which Mn(II) binding is perturbed by mutagenesis of Glu-101 and Glu-280, which coordinate the metal in the N-terminal and C-terminal domains, respectively. We now demonstrate that decarboxylase activity and total manganese content are sensitive to modifications in either metal-binding glutamate residue. These findings, in combination with EPR measurements, raise the possibility that the C-terminal Mn(II) center can catalyze the decarboxylation reaction. Further support for this conclusion has been provided from a combination of in vivo and in vitro strategies for preparing wild-type OxDC in which Mn(II) is incorporated to a variety of extents. Kinetic characterization of these variants shows that OxDC activity is linearly correlated with manganese content, as might be expected if both sites can catalyze the breakdown of oxalate into formate and CO(2). These studies also represent the first unequivocal demonstration that OxDC activity is uniquely mediated by manganese.
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Affiliation(s)
- Ellen W. Moomaw
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | | | - Patricia Moussatche
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-3706
| | - Inés García-Rubio
- Laboratorium fur Physikalische Chemie, ETH Zurich, CH-8043 Zurich-Hönggerberg, Switzerland
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Richards NGJ. Shining a light on post-translational modification. HFSP J 2009; 2:57-60. [PMID: 19404471 DOI: 10.2976/1.2889161] [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] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Indexed: 11/19/2022]
Abstract
Post-translational modification, such as phosphorylation or glycosylation, provides a mechanism for increasing the diversity of protein structures in the cell and regulating biological activity. In addition, such modifications may result in the localization of proteins to specific cellular organelles, with incorrect targeting being associated with a number of diseases. The simplest strategy to identify the functional importance of post-translational modifications is to use mutagenesis methods to replace the residue that is post-translationally modified by one that cannot undergo the relevant chemical transformation. Merely causing "loss of function" does not, however, address questions concerning how cellular function depends on the timing of post-translational changes andor the movement of modified proteins between organelles. The recent demonstration that genetically encoded "photocaged" proteins can be employed to resolve such issues therefore represents an exciting advance in this research area, and is an elegant illustration of the power of combining the power of chemical synthesis and methods for manipulating the biological machinery of protein synthesis.
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Affiliation(s)
- Nigel G J Richards
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611-7200, USA
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49
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Toyota CG, Berthold CL, Gruez A, Jónsson S, Lindqvist Y, Cambillau C, Richards NGJ. Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase. J Bacteriol 2008; 190:2556-64. [PMID: 18245280 PMCID: PMC2293189 DOI: 10.1128/jb.01823-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/25/2008] [Indexed: 01/29/2023] Open
Abstract
The yfdXWUVE operon appears to encode proteins that enhance the ability of Escherichia coli MG1655 to survive under acidic conditions. Although the molecular mechanisms underlying this phenotypic behavior remain to be elucidated, findings from structural genomic studies have shown that the structure of YfdW, the protein encoded by the yfdW gene, is homologous to that of the enzyme that mediates oxalate catabolism in the obligate anaerobe Oxalobacter formigenes, O. formigenes formyl coenzyme A transferase (FRC). We now report the first detailed examination of the steady-state kinetic behavior and substrate specificity of recombinant, wild-type YfdW. Our studies confirm that YfdW is a formyl coenzyme A (formyl-CoA) transferase, and YfdW appears to be more stringent than the corresponding enzyme (FRC) in Oxalobacter in employing formyl-CoA and oxalate as substrates. We also report the effects of replacing Trp-48 in the FRC active site with the glutamine residue that occupies an equivalent position in the E. coli protein. The results of these experiments show that Trp-48 precludes oxalate binding to a site that mediates substrate inhibition for YfdW. In addition, the replacement of Trp-48 by Gln-48 yields an FRC variant for which oxalate-dependent substrate inhibition is modified to resemble that seen for YfdW. Our findings illustrate the utility of structural homology in assigning enzyme function and raise the question of whether oxalate catabolism takes place in E. coli upon the up-regulation of the yfdXWUVE operon under acidic conditions.
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Affiliation(s)
- Cory G Toyota
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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50
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Berthold CL, Toyota CG, Richards NGJ, Lindqvist Y. Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase. J Biol Chem 2007; 283:6519-29. [PMID: 18162462 DOI: 10.1074/jbc.m709353200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transferase has a unique three-dimensional fold composed of two interlaced subunits locked together like rings of a chain. We here present an intermediate in the reaction, formyl-CoA transferase containing the covalent beta-aspartyl-CoA thioester, adopting different conformations in the two active sites of the dimer, which was identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid. The formation of the enzyme-CoA thioester was also confirmed by mass spectrometric data. Further structural data include a trapped aspartyl-formyl anhydride protected by a glycine loop closing down over the active site. In a crystal structure of the beta-aspartyl-CoA thioester of an inactive mutant variant, oxalate was found bound to the open conformation of the glycine loop. Together with hydroxylamine trapping experiments and kinetic as well as mutagenesis data, the structures of these formyl-CoA transferase complexes provide new information on the Class III CoA-transferase family and prompt redefinition of the catalytic steps and the modified reaction mechanism of formyl-CoA transferase proposed here.
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Affiliation(s)
- Catrine L Berthold
- Department of Medical Biochemistry and Biophysics, Molecular Structural Biology, Karolinska Institutet, Stockholm, Sweden
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