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Monselise EBI, Vyazmensky M, Scherf T, Batushansky A, Fishov I. D-Glutamate production by stressed Escherichia coli gives a clue for the hypothetical induction mechanism of the ALS disease. Sci Rep 2024; 14:18247. [PMID: 39107374 PMCID: PMC11303787 DOI: 10.1038/s41598-024-68645-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
In the search for the origin of Amyotrophic Lateral Sclerosis disease (ALS), we hypothesized earlier (Monselise, 2019) that D-amino acids produced by stressed microbiome may serve as inducers of the disease development. Many examples of D-amino acid accumulation under various stress conditions were demonstrated in prokaryotic and eukaryotic cells. In this work, wild-type Escherichia coli, members of the digestive system, were subjected to carbon and nitrogen starvation stress. Using NMR and LC-MS techniques, we found for the first time that D-glutamate accumulated in the stressed bacteria but not in control cells. These results together with the existing knowledge, allow us to suggest a new insight into the pathway of ALS development: D-glutamate, produced by the stressed microbiome, induces neurobiochemical miscommunication setting on C1q of the complement system. Proving this insight may have great importance in preventive medicine of such MND modern-age diseases as ALS, Alzheimer, and Parkinson.
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Affiliation(s)
- Edna Ben-Izhak Monselise
- Department of Life Science, Bergman Campus, Ben-Gurion University of the Negev, 8441901, Beer-Sheva, Israel.
| | - Maria Vyazmensky
- Department of Life Science, Bergman Campus, Ben-Gurion University of the Negev, 8441901, Beer-Sheva, Israel
| | - Tali Scherf
- Department of Chemical Research Support, The Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Albert Batushansky
- Ilse Katz Institute for Nanoscale Science & Technology, Marcus Campus, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Itzhak Fishov
- Department of Life Science, Bergman Campus, Ben-Gurion University of the Negev, 8441901, Beer-Sheva, Israel.
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Pawar A, Konwar C, Jha P, Kant R, Chopra M, Chaudhry U, Saluja D. Bactericidal activity of esculetin is associated with impaired cell wall synthesis by targeting glutamate racemase of Neisseria gonorrhoeae. Mol Divers 2023:10.1007/s11030-023-10745-0. [PMID: 37880544 DOI: 10.1007/s11030-023-10745-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023]
Abstract
Neisseria gonorrhoeae (NG), the causative organism of gonorrhea, has been classified by the World Health Organization as 'Priority' two organism owing to its increased resistance to antibiotics and even failure of recommended dual therapy with ceftriaxone and azithromycin. As a result, the general and reproductive health of infected individuals is severely compromised. The imminent public health catastrophe of antimicrobial-resistant gonococci cannot be understated, as t he of severe complications and sequelae of infection are not only increasing but their treatment has also become more expensive. Tenacious attempts are underway to discover novel drug targets as well as new drugs to fight against NG. Therefore, a considerable number of phytochemicals have been tested for their remedial intercession via targeting bacterial proteins. The MurI gene encodes for an enzyme called glutamate racemase (MurI) that is primarily involved in peptidoglycan (PG) biosynthesis and is specific to the bacterial kingdom and hence can be exploited as a potential drug target for the treatment of bacterial diseases. Accordingly, diverse families of phytochemicals were screened in silico for their binding affinity with N. Gonorrhoeae MurI (NG-MurI) protein. Esculetin, one of the shortlisted compounds, was evaluated for its functional, structural, and anti-bacterial activity. Treatment with esculetin resulted in growth inhibition, cell wall damage, and altered permeability as revealed by fluorescence and electron microscopy. Furthermore, esculetin inhibited the racemization activity of recombinant, purified NG-MurI protein, one of the enzymes required for peptidoglycan biosynthesis. Our results suggest that esculetin could be further explored as a lead compound for developing new drug molecules against multidrug-resistant strains.
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Affiliation(s)
- Alka Pawar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Chandrika Konwar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Prakash Jha
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Ravi Kant
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Madhu Chopra
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, 110075, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
- Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
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Bearne SL. Design and evaluation of substrate-product analog inhibitors for racemases and epimerases utilizing a 1,1-proton transfer mechanism. Methods Enzymol 2023; 690:397-444. [PMID: 37858537 DOI: 10.1016/bs.mie.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Racemases and epimerases catalyze the inversion of stereochemistry at asymmetric carbon atoms to generate stereoisomers that often play important roles in normal and pathological physiology. Consequently, there is interest in developing inhibitors of these enzymes for drug discovery. A strategy for the rational design of substrate-product analog (SPA) inhibitors of racemases and epimerases utilizing a direct 1,1-proton transfer mechanism is elaborated. This strategy assumes that two groups on the asymmetric carbon atom remain fixed at active-site binding determinants, while the hydrogen and third, motile group move during catalysis, with the latter potentially traveling between an R- and S-pocket at the active site. SPAs incorporate structural features of the substrate and product, often with geminal disubstitution on the asymmetric carbon atom to simultaneously present the motile group to both the R- and S-pockets. For racemases operating on substrates bearing three polar groups (glutamate, aspartate, and serine racemases) or with compact, hydrophobic binding pockets (proline racemase), substituent motion is limited and the design strategy furnishes inhibitors with poor or modest binding affinities. The approach is most successful when substrates have a large, motile hydrophobic group that binds at a plastic and/or capacious hydrophobic site. Potent inhibitors were developed for mandelate racemase, isoleucine epimerase, and α-methylacyl-CoA racemase using the SPA inhibitor design strategy, exhibiting binding affinities ranging from substrate-like to exceeding that of the substrate by 100-fold. This rational approach for designing inhibitors of racemases and epimerases having the appropriate active-site architectures is a useful strategy for furnishing compounds for drug development.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
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4
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Bearne SL, Hayden JA. Application of circular dichroism-based assays to racemases and epimerases: Recognition and catalysis of reactions of chiral substrates by mandelate racemase. Methods Enzymol 2023; 685:127-169. [PMID: 37245900 DOI: 10.1016/bs.mie.2023.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Racemases and epimerases have attracted much interest because of their astonishing ability to catalyze the rapid α-deprotonation of carbon acid substrates with high pKa values (∼13-30) leading to the formation of d-amino acids or various carbohydrate diastereomers that serve important roles in both normal physiology and pathology. Enzymatic assays to measure the initial rates of reactions catalyzed by these enzymes are discussed using mandelate racemase (MR) as an example. For MR, a convenient, rapid, and versatile circular dichroism (CD)-based assay has been used to determine the kinetic parameters accompanying the MR-catalyzed racemization of mandelate and alternative substrates. This direct, continuous assay permits real time monitoring of reaction progress, the rapid determination of initial velocities, and immediate recognition of anomalous behaviors. MR recognizes chiral substrates primarily through interactions of the phenyl ring of (R)- or (S)-mandelate with the hydrophobic R- or S-pocket at the active site, respectively. During catalysis, the carboxylate and α-hydroxyl groups of the substrate remain fixed in place through interactions with the Mg2+ ion and multiple H-bonding interactions, while the phenyl ring moves between the R- and S-pockets. The minimal requirements for the substrate appear to be the presence of a glycolate or glycolamide moiety, and a hydrophobic group of limited size that can stabilize the carbanionic intermediate through resonance or strong inductive effects. Similar CD-based assays may be applied to determine the activity of other racemases or epimerases with proper consideration of the molar ellipticity, wavelength, overall absorbance of the sample, and the light pathlength.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
| | - Joshua A Hayden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Lloyd MD, Yevglevskis M, Nathubhai A, James TD, Threadgill MD, Woodman TJ. Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition. Chem Soc Rev 2021; 50:5952-5984. [PMID: 34027955 PMCID: PMC8142540 DOI: 10.1039/d0cs00540a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.
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Affiliation(s)
- Matthew D Lloyd
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Maksims Yevglevskis
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and CatSci Ltd., CBTC2, Capital Business Park, Wentloog, Cardiff CF3 2PX, UK
| | - Amit Nathubhai
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and University of Sunderland, School of Pharmacy & Pharmaceutical Sciences, Sciences Complex, Sunderland SR1 3SD, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK and School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, People's Republic of China
| | - Michael D Threadgill
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. and Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth SY23 3BY, UK
| | - Timothy J Woodman
- Drug & Target Discovery, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Identification of an l-serine/l-threonine dehydratase with glutamate racemase activity in mammals. Biochem J 2020; 477:4221-4241. [DOI: 10.1042/bcj20200721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
Recent investigations have shown that multiple d-amino acids are present in mammals and these compounds have distinctive physiological functions. Free d-glutamate is present in various mammalian tissues and cells and in particular, it is presumably correlated with cardiac function, and much interest is growing in its unique metabolic pathways. Recently, we first identified d-glutamate cyclase as its degradative enzyme in mammals, whereas its biosynthetic pathway in mammals is unclear. Glutamate racemase is a most probable candidate, which catalyzes interconversion between d-glutamate and l-glutamate. Here, we identified the cDNA encoding l-serine dehydratase-like (SDHL) as the first mammalian clone with glutamate racemase activity. This rat SDHL had been deposited in mammalian databases as a protein of unknown function and its amino acid sequence shares ∼60% identity with that of l-serine dehydratase. Rat SDHL was expressed in Escherichia coli, and the enzymatic properties of the recombinant were characterized. The results indicated that rat SDHL is a multifunctional enzyme with glutamate racemase activity in addition to l-serine/l-threonine dehydratase activity. This clone is hence abbreviated as STDHgr. Further experiments using cultured mammalian cells confirmed that d-glutamate was synthesized and l-serine and l-threonine were decomposed. It was also found that SDHL (STDHgr) contributes to the homeostasis of several other amino acids.
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Bearne SL. Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases. Chemistry 2020; 26:10367-10390. [DOI: 10.1002/chem.201905826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/09/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry & Molecular BiologyDepartment of ChemistryDalhousie University Halifax, Nova Scotia B3H 4R2 Canada
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Witkin KR, Vance NR, Caldwell C, Li Q, Yu L, Spies MA. An Atomistic Understanding of Allosteric Inhibition of Glutamate Racemase: a Dampening of Native Activation Dynamics. ChemMedChem 2020; 15:376-384. [PMID: 31876113 PMCID: PMC7337235 DOI: 10.1002/cmdc.201900642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/11/2019] [Indexed: 11/07/2022]
Abstract
Glutamate racemases (GR) are members of the family of bacterial enzymes known as cofactor-independent racemases and epimerases and catalyze the stereoinversion of glutamate. D-amino acids are universally important for the proper construction of viable bacterial cell walls, and thus have been repeatedly validated as attractive targets for novel antimicrobial drug design. Significant aspects of the mechanism of this challenging stereoinversion remain unknown. The current study employs a combination of MD and QM/MM computational approaches to show that the GR from H. pylori must proceed via a pre-activation step, which is dependent on the enzyme's flexibility. This mechanism is starkly different from previously proposed mechanisms. These findings have immediate pharmaceutical relevance, as the H. pylori GR enzyme is a very attractive allosteric drug target. The results presented in this study offer a distinctly novel understanding of how AstraZeneca's lead series of inhibitors cripple the H. pylori GR's native motions, via prevention of this critical chemical pre-activation step. Our experimental studies, using SPR, fluorescence and NMR WaterLOGSY, show that H. pylori GR is not inhibited by the uncompetitive mechanism originally put forward by Lundqvist et al.. The current study supports a deep connection between native enzyme motions and chemical reactivity, which has strong relevance to the field of allosteric drug discovery.
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Affiliation(s)
- Katie R Witkin
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Colleen Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Quinn Li
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Liping Yu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
- NMR Core Facility, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
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9
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Screening of natural compounds that targets glutamate racemase of Mycobacterium tuberculosis reveals the anti-tubercular potential of flavonoids. Sci Rep 2020; 10:949. [PMID: 31969615 PMCID: PMC6976638 DOI: 10.1038/s41598-020-57658-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/17/2019] [Indexed: 01/23/2023] Open
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis (MTB), a highly infectious disease accounting for nearly 1.5 million deaths every year and has been a major global concern. Moreover, resistance to anti-TB drugs is an arduous obstacle to effective prevention, TB care and management. Therefore, incessant attempts are being made to identify novel drug targets and newer anti-tubercular drugs to fight with this deadly pathogen. Increasing resistance, adverse effects and costly treatment by conventional therapeutic agents have been inclining the researchers to search for an alternative source of medicine. In this regard natural compounds have been exploited extensively for their therapeutic interventions targeting cellular machinery of MTB. Glutamate racemase (MurI) is an enzyme involved in peptidoglycan (PG) biosynthesis and has become an attractive target due to its moonlighting property. We screened various classes of natural compounds using computational approach for their binding to MTB-MurI. Shortlisted best docked compounds were evaluated for their functional, structural and anti-mycobacterial activity. The results showed that two flavonoids (naringenin and quercetin) exhibited best binding affinity with MTB-MurI and inhibited the racemization activity with induced structural perturbation. In addition, fluorescence and electron microscopy were employed to confirm the membrane and cell wall damages in mycobacterial cells on exposure to flavonoids. Together, these observations could provide impetus for further research in better understanding of anti-tubercular mechanisms of flavonoids and establishing them as lead molecules for TB treatment.
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Wang X, Chen C, Shen T, Zhang J. Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159. PeerJ 2019; 7:e8300. [PMID: 31875162 PMCID: PMC6927343 DOI: 10.7717/peerj.8300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/26/2019] [Indexed: 01/03/2023] Open
Abstract
Background Glutamate racemase (MurI) is a cofactor-independent enzyme that is essential to the bacterial peptidoglycan biosynthesis pathway and has therefore been considered an attractive target for the development of antimicrobial drugs. While in our previous study the essentiality of the murI gene was shown in Streptococcus mutans, the primary aetiologic agent of human dental caries, studies on S. mutans MurI have not yet provided definitive results. This study aimed to produce and characterize the biochemical properties of the MurI from the S. mutans UA159 genome. Methods Structure characterization prediction and multiple sequence alignment were performed by bioinformatic analysis. Recombinant His6-tagged S. mutans MurI was overexpressed in the expression vector pColdII and further purified using a Ni2+ affinity chromatography method. Protein solubility, purity and aggregation state were analyzed by SDS–PAGE, Western blotting, native PAGE and SEC-HPLC. Kinetic parameters were assessed by a circular dichroism (CD) assay. Kinetic constants were calculated based on the curve fit for the Michaelis–Menten equation. The effects of temperature and pH on enzymatic activity were determined by a series of coupled enzyme reaction mixtures. Results The glutamate racemase gene from S. mutans UA159 was amplified by PCR, cloned and expressed in Escherichia coli BL21 (DE3). The 264-amino-acid protein, as a mixture of dimeric and monomeric enzymes, was purified to electrophoretic homogeneity. In the CD assay, S. mutans MurI displayed unique kinetic parameters (Km, d-Glu→l-Glu = 0.3631 ± 0.3205 mM, Vmax, d-Glu→l-Glu = 0.1963 ± 0.0361 mM min−1, kcat, d-Glu→l-Glu = 0.0306 ± 0.0065 s−1, kcat/Km,d-Glu→l-Glu = 0.0844 ± 0.0128 s−1 mM−1, with d-glutamate as substrate; Km, l-Glu→d-Glu = 0.8077 ± 0.5081 mM, Vmax, l-Glu→d-Glu = 0.2421 ± 0.0418 mM min−1, kcat,l-Glu→d-Glu = 0.0378 ± 0.0056 s−1, kcat/Km,l-Glu→d-Glu = 0.0468 ± 0.0176 s−1 mM−1, with l-glutamate as substrate). S. mutans MurI possessed an assay temperature optimum of 37.5 °C and its optimum pH was 8.0. Conclusion The findings of this study provide insight into the structure and biochemical traits of the glutamate racemase in S. mutans and supply a conceivable guideline for employing glutamate racemase in anti-caries drug design.
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Affiliation(s)
- Xiangzhu Wang
- Department of Operative Dentistry and Endodotics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Chanchan Chen
- Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Ting Shen
- Department of Operative Dentistry and Endodotics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
| | - Jiangying Zhang
- Department of Operative Dentistry and Endodotics, Xiangya School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, China
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Opel-Reading H, Mortuza R, Krause K. Detection of D-glutamate Production from the Dual Function Enzyme, 4-amino-4-deoxychorismate Lyase/D-amino Acid Transaminase, in Mycobacterium smegmatis. Bio Protoc 2019; 9:e3135. [DOI: 10.21769/bioprotoc.3135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 11/27/2018] [Accepted: 12/14/2018] [Indexed: 11/02/2022] Open
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Vance NR, Witkin KR, Rooney PW, Li Y, Pope M, Spies MA. Elucidating the Catalytic Power of Glutamate Racemase by Investigating a Series of Covalent Inhibitors. ChemMedChem 2018; 13:2514-2521. [PMID: 30264520 DOI: 10.1002/cmdc.201800592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 12/29/2022]
Abstract
The application of covalent inhibitors has experienced a renaissance within drug discovery programs in the last decade. To leverage the superior potency and drug target residence time of covalent inhibitors, there have been extensive efforts to develop highly specific covalent modifications to decrease off-target liabilities. Herein, we present a series of covalent inhibitors of an antimicrobial drug target, glutamate racemase, discovered through structure-based virtual screening. A combination of enzyme kinetics, mass spectrometry, and surface-plasmon resonance experiments details a highly specific 1,4-conjugate addition of a small-molecule inhibitor with a catalytic cysteine of glutamate racemase. Molecular dynamics simulations and quantum mechanics-molecular mechanics geometry optimizations reveal the chemistry of the conjugate addition. Two compounds from this series of inhibitors display antimicrobial potency similar to β-lactam antibiotics, with significant activity against methicillin-resistant S. aureus strains. This study elucidates a detailed chemical rationale for covalent inhibition and provides a platform for the development of antimicrobials with a novel mechanism of action against a target in the cell wall biosynthesis pathway.
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Affiliation(s)
- Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Katie R Witkin
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Patrick W Rooney
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Yalan Li
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - Marshall Pope
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
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13
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Pawar A, Jha P, Konwar C, Chaudhry U, Chopra M, Saluja D. Ethambutol targets the glutamate racemase of Mycobacterium tuberculosis—an enzyme involved in peptidoglycan biosynthesis. Appl Microbiol Biotechnol 2018; 103:843-851. [DOI: 10.1007/s00253-018-9518-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 12/11/2022]
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14
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Shey RA, Ghogomu SM, Njume FN, Gainkam LOT, Poelvoorde P, Mutesa L, Robert A, Humblet P, Munyampundu JP, Kamgno J, Lelubre C, Vanhamme L, Souopgui J. Prediction and validation of the structural features of Ov58GPCR, an immunogenic determinant of Onchocerca volvulus. PLoS One 2018; 13:e0202915. [PMID: 30256790 PMCID: PMC6157839 DOI: 10.1371/journal.pone.0202915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/11/2018] [Indexed: 11/18/2022] Open
Abstract
Onchocerciasis is a severely debilitating yet neglected tropical disease (NTD) that creates social stigma, generates and perpetuates poverty, and leads ultimately in some cases to irreversible unilateral or bilateral blindness if untreated. Consequently, the disease is a major impediment to socioeconomic development. Many control programs have been launched for the disease with moderate successes achieved. This mitigated hit is partially due to the lingering need for reliable, non-invasive and easily applicable tools for mapping endemic regions and post-elimination surveillance. In this work, bioinformatics analyses combined with immunological assays were applied in a bid to develop potential tools for diagnosis and assessing the success of drug treatment programs. We report that (i) the O. volvulus antigen, Ov58GPCR is a G-protein coupled receptor (GPCR) conserved in related nematodes, (ii) synthetic peptides predicted to be in the extracellular domain (ECD) of Ov58GPCR are indeed immunogenic epitopes in actively-infected individuals, (iii) synthetic peptide cocktails discriminate between actively-infected individuals, treated individuals and healthy African controls, (iv) polyclonal antibodies against one of the peptides or against the bacterially-expressed ECD reacted specifically with the native antigen of O. volvulus total and surface extracts, (v) Ov58GPCR is transcribed in both larvae and adult parasite stages, (vi) IgG and IgE responses to the recombinant ECD decline with ivermectin treatment. All these findings suggest that the extracellular domain and synthetic peptides of Ov58GPCR, as well as the specific immune response generated could be harnessed in the context of disease diagnosis and surveillance.
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Affiliation(s)
- Robert Adamu Shey
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Faculty of Science, University of Buea, Buea, Cameroon
| | - Lea Olive Tchouate Gainkam
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Philippe Poelvoorde
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Annie Robert
- Faculté de santé publique, Institut de recherche expérimentale et clinique, Pôle d'épidémiologie et biostatistique, Université Catholique de Louvain, Clos Chapelle-aux-champs, Woluwe-Saint-Lambert, Belgium
| | - Perrine Humblet
- École de santé publique, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jean-Pierre Munyampundu
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Joseph Kamgno
- Department of Epidemiology, Centre for research on filariasis and other tropical diseases, (CRFilMT), Yaoundé, Cameroon
| | - Christophe Lelubre
- Laboratoire de Médecine Expérimentale, Université Libre de Bruxelles (ULB) - Unité 222, CHU Charleroi (Hôpital André Vésale), Montigny-Le-Tilleul, Belgium
| | - Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Gosselies, Hainaut, Belgium
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15
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Mackie J, Kumar H, Bearne SL. Changes in quaternary structure cause a kinetic asymmetry of glutamate racemase-catalyzed homocysteic acid racemization. FEBS Lett 2018; 592:3399-3413. [PMID: 30194685 DOI: 10.1002/1873-3468.13248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/30/2018] [Accepted: 08/24/2018] [Indexed: 11/07/2022]
Abstract
Glutamate racemases (GR) catalyze the racemization of d- and l-glutamate and are targets for the development of antibiotics. We demonstrate that GR from the periodontal pathogen Fusobacterium nucleatum (FnGR) catalyzes the racemization of d-homocysteic acid (d-HCA), while l-HCA is a poor substrate. This enantioselectivity arises because l-HCA perturbs FnGR's monomer-dimer equilibrium toward inactive monomer. The inhibitory effect of l-HCA may be overcome by increasing the total FnGR concentration or by adding glutamate, but not by blocking access to the active site through site-directed mutagenesis, suggesting that l-HCA binds at an allosteric site. This phenomenon is also exhibited by GR from Bacillus subtilis, suggesting that enantiospecific, "substrate"-induced dissociation of oligomers to form inactive monomers may furnish a new inhibition strategy.
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Affiliation(s)
- Joanna Mackie
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Himank Kumar
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Department of Chemistry, Dalhousie University, Halifax, Canada
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16
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Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery. Biochem J 2016; 473:1267-80. [PMID: 26964898 DOI: 10.1042/bcj20160186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022]
Abstract
Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed. In the present study, we have determined the protein crystal structures of MurI from both M. tuberculosis and Mycobacterium smegmatis in complex with D-glutamate to 2.3 Å and 1.8 Å resolution respectively. These structures are conserved, but reveal differences in their active site architecture compared with that of other MurI structures. Furthermore, compounds designed to target other glutamate racemases have been screened but do not inhibit mycobacterial MurI, suggesting that a new drug design effort will be needed to develop inhibitors. A new type of MurI dimer arrangement has been observed in both structures, and this arrangement becomes the third biological dimer geometry for MurI found to date. The mycobacterial MurI dimer is tightly associated, with a KD in the nanomolar range. The enzyme binds D- and L-glutamate specifically, but is inactive in solution unless the dimer interface is mutated. We created triple mutants of this interface in the M. smegmatis glutamate racemase (D26R/R105A/G194R or E) that have appreciable activity (kcat=0.056-0.160 min(-1) and KM=0.26-0.51 mM) and can be utilized to screen proposed antimicrobial candidates for inhibition.
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17
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Yevglevskis M, Lee GL, Sun J, Zhou S, Sun X, Kociok-Köhn G, James TD, Woodman TJ, Lloyd MD. A study on the AMACR catalysed elimination reaction and its application to inhibitor testing. Org Biomol Chem 2016; 14:612-622. [PMID: 26537174 PMCID: PMC4718014 DOI: 10.1039/c5ob01541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/27/2015] [Indexed: 12/15/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyses a key step in the degradation of branched-chain fatty acids and is important for the pharmacological activation of Ibuprofen and related drugs. Levels of AMACR are increased in prostate and other cancers, and it is a drug target. Development of AMACR as a drug target is hampered by lack of a convenient assay. AMACR irreversibly catalyses the elimination of HF from 3-fluoro-2-methylacyl-CoA substrates, and this reaction was investigated for use as an assay. Several known inhibitors and alternative substrates reduced conversion of 3-fluoro-2-methyldecanoyl-CoA by AMACR, as determined by (1)H NMR. The greatest reduction of activity was observed with known potent inhibitors. A series of novel acyl-CoA esters with aromatic side chains were synthesised for testing as chromophoric substrates. These acyl-CoA esters were converted to unsaturated products by AMACR, but their use was limited by non-enzymatic elimination. Fluoride sensors were also investigated as a method of quantifying released fluoride and thus AMACR activity. These sensors generally suffered from high background signal and lacked reproducibility under the assay conditions. In summary, the elimination reaction can be used to characterise inhibitors, but it was not possible to develop a convenient colorimetric or fluorescent assay using 3-fluoro-2-methylacyl-CoA substrates.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Guat L. Lee
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Jenny Sun
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Shiyi Zhou
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Xiaolong Sun
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Gabriele Kociok-Köhn
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Tony D. James
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Timothy J. Woodman
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Matthew D. Lloyd
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
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18
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Ahn JW, Chang JH, Kim KJ. Structural basis for an atypical active site of an L-aspartate/glutamate-specific racemase from Escherichia coli. FEBS Lett 2015; 589:3842-7. [PMID: 26555188 DOI: 10.1016/j.febslet.2015.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 11/15/2022]
Abstract
We determined the crystal structure of EcL-DER to elucidate protein function and substrate specificity. Unlike other asp/glu racemases, EcL-DER has an unbalanced pair of catalytic residues, Thr83/Cys197, at the active site that is crucial for L- to D-unidirectional racemase activity. EcL-DER exhibited racemase activity for both L-glutamate and L-aspartate, but had threefold higher activity for L-glutamate. Based on the structure of the EcL-DER(C197S) mutant in complex with L-glutamate, we determined the binding mode of the L-glutamate substrate in EcL-DER and provide a structural basis for how the protein utilizes L-glutamate as a main substrate. The unidirectionality, despite an equilibrium constant of unity, can be understood in terms of the Haldane relationship.
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Affiliation(s)
- Jae-Woo Ahn
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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19
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Investigation of the essentiality of glutamate racemase in Mycobacterium smegmatis. J Bacteriol 2014; 196:4239-44. [PMID: 25246478 DOI: 10.1128/jb.02090-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mycobacterial cell wall frequently has been used as a target for drug development, and d-glutamate, synthesized by glutamate racemase (MurI), is an important component of peptidoglycan. While the essentiality of the murI gene has been shown in several bacterial species, including Escherichia coli, Bacillus anthracis, and Streptococcus pneumoniae, studies in mycobacteria have not yet provided definitive results. This study aimed to determine whether murI is indeed essential and can serve as a possible target for structure-aided drug design. We have achieved this goal by creating a ΔmurI strain of Mycobacterium smegmatis, a close relative of Mycobacterium tuberculosis. The deletion of the murI gene in M. smegmatis could be achieved only in minimal medium supplemented with D-glutamate, demonstrating that MurI is essential for growth and that glutamate racemase is the only source of D-glutamate for peptidoglycan synthesis in M. smegmatis.
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20
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Ollivaux C, Soyez D, Toullec JY. Biogenesis of d
-amino acid containing peptides/proteins: where, when and how? J Pept Sci 2014; 20:595-612. [DOI: 10.1002/psc.2637] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Céline Ollivaux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
| | - Daniel Soyez
- Sorbonne Universités, UPMC Univ Paris 06, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
- CNRS, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
| | - Jean-Yves Toullec
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
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21
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Bacterial synthesis of D-amino acids. Appl Microbiol Biotechnol 2014; 98:5363-74. [PMID: 24752840 DOI: 10.1007/s00253-014-5726-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/25/2014] [Indexed: 12/30/2022]
Abstract
Recent work has shed light on the abundance and diversity of D-amino acids in bacterial extracellular/periplasmic molecules, bacterial cell culture, and bacteria-rich environments. Within the extracellular/periplasmic space, D-amino acids are necessary components of peptidoglycan, and disruption of their synthesis leads to cell death. As such, enzymes responsible for D-amino acid synthesis are promising targets for antibacterial compounds. Further, bacteria are shown to incorporate a diverse collection of D-amino acids into their peptidoglycan, and differences in D-amino acid incorporation may occur in response to differences in growth conditions. Certain D-amino acids can accumulate to millimolar levels in cell culture, and their synthesis is proposed to foretell movement from exponential growth phase into stationary phase. While enzymes responsible for synthesis of D-amino acids necessary for peptidoglycan (D-alanine and D-glutamate) have been characterized from a number of different bacteria, the D-amino acid synthesis enzymes characterized to date cannot account for the diversity of D-amino acids identified in bacteria or bacteria-rich environments. Free D-amino acids are synthesized by racemization or epimerization at the α-carbon of the corresponding L-amino acid by amino acid racemase or amino acid epimerase enzymes. Additionally, D-amino acids can be synthesized by stereospecific amination of α-ketoacids. Below, we review the roles of D-amino acids in bacterial physiology and biotechnology, and we describe the known mechanisms by which they are synthesized by bacteria.
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22
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23
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Böhmer N, Dautel A, Eisele T, Fischer L. Recombinant expression, purification and characterisation of the native glutamate racemase from Lactobacillus plantarum NC8. Protein Expr Purif 2013; 88:54-60. [DOI: 10.1016/j.pep.2012.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/21/2012] [Accepted: 11/23/2012] [Indexed: 11/29/2022]
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24
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A ligand-based approach for enhancing the pharmacokinetic profile of highly charged antibacterial agents. Med Chem Res 2012. [DOI: 10.1007/s00044-010-9538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Jiao W, Parker EJ. Using a combination of computational and experimental techniques to understand the molecular basis for protein allostery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 87:391-413. [PMID: 22607762 DOI: 10.1016/b978-0-12-398312-1.00013-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Allostery is the process by which remote sites of a system are energetically coupled to elicit a functional response. The early models of allostery such as the Monod-Wyman-Changeux model and the Koshland-Némethy-Filmer model explain the allosteric behavior of multimeric proteins. However, these models do not explain how allostery arises from atomic level in detail. Recent developments in computational methods and experimental techniques have led the beginning of a new age in studying allostery. The combination of computational methods and experiments is a powerful research approach to help answering questions regarding allosteric mechanism at atomic resolution. In this review, three case studies are discussed to illustrate how this combined approach helps to increase our understanding of protein allostery.
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Affiliation(s)
- Wanting Jiao
- Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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26
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Fisch F, Fleites CM, Delenne M, Baudendistel N, Hauer B, Turkenburg JP, Hart S, Bruce NC, Grogan G. A covalent succinylcysteine-like intermediate in the enzyme-catalyzed transformation of maleate to fumarate by maleate isomerase. J Am Chem Soc 2010; 132:11455-7. [PMID: 20677745 DOI: 10.1021/ja1053576] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Maleate isomerase (MI), a member of the Asp/Glu racemase superfamily, catalyzes cis-trans isomerization of the C2-C3 double bond in maleate to yield fumarate. Mutational studies, in conjunction with the structure of the C194A mutant of Nocardia farcinica MI cocrystallized with maleate, have revealed an unprecedented mode of catalysis for the superfamily in which the isomerization reaction is initiated by nucleophilic attack of cysteine at the double bond, yielding a covalent succinylcysteine-like intermediate.
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Affiliation(s)
- Florian Fisch
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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27
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Gavina JMA, White CE, Finan TM, Britz-McKibbin P. Determination of 4-hydroxyproline-2-epimerase activity by capillary electrophoresis: A stereoselective platform for inhibitor screening of amino acid isomerases. Electrophoresis 2010; 31:2831-7. [DOI: 10.1002/elps.201000187] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Nara TY, Togashi H, Sekikawa C, Inoh K, Hisamatsu K, Sakaguchi K, Mizukami F, Tsunoda T. Functional immobilization of racemase by adsorption on folded-sheet mesoporous silica. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Kinetic characterization and quaternary structure of glutamate racemase from the periodontal anaerobe Fusobacterium nucleatum. Arch Biochem Biophys 2009; 491:16-24. [DOI: 10.1016/j.abb.2009.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/11/2009] [Accepted: 09/15/2009] [Indexed: 11/17/2022]
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30
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Spies MA, Reese JG, Dodd D, Pankow KL, Blanke SR, Baudry J. Determinants of catalytic power and ligand binding in glutamate racemase. J Am Chem Soc 2009; 131:5274-84. [PMID: 19309142 DOI: 10.1021/ja809660g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glutamate racemases (EC 5.1.1.3) catalyze the cofactor-independent stereoinversion of D- and L-glutamate and are important for viability in several gram-negative and -positive bacteria. As the only enzyme involved in the stereoinversion of L- to D-glutamate for peptidoglycan biosynthesis, glutamate racemase is an attractive target for the design of antibacterial agents. However, the development of competitive tight-binding inhibitors has been problematic and highly species specific. Despite a number of recent crystal structures of cofactor-independent epimerases and racemases, cocrystallized with substrates or substrate analogues, the source of these enzymes' catalytic power and their ability to acidify the C alpha of amino acids remains unknown. The present integrated computational and experimental study focuses on the glutamate racemase from Bacillus subtilis (RacE). A particular focus is placed on the interaction of the glutamate carbanion intermediate with RacE. Results suggest that the reactive form of the RacE-glutamate carbanion complex, vis-à-vis proton abstraction from C alpha, is significantly different than the RacE-D-glutamate complex on the basis of the crystal structure and possesses dramatically stronger enzyme-ligand interaction energy. In silico and experimental site-directed mutagenesis indicates that the strength of the RacE-glutamate carbanion interaction energy is highly distributed among numerous electrostatic interactions in the active site, rather than being dominated by strong hydrogen bonds. Results from this study are important for laying the groundwork for discovery and design of high-affinity ligands to this class of cofactor-independent racemases.
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Affiliation(s)
- M Ashley Spies
- Department of Biochemistry, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA.
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31
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Sengupta S, Ghosh S, Nagaraja V. Moonlighting function of glutamate racemase from Mycobacterium tuberculosis: racemization and DNA gyrase inhibition are two independent activities of the enzyme. MICROBIOLOGY-SGM 2008; 154:2796-2803. [PMID: 18757813 DOI: 10.1099/mic.0.2008/020933-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glutamate racemase (MurI) provides d-glutamate, a key building block in the peptidoglycan of the bacterial cell wall. Besides having a crucial role in cell wall biosynthesis, MurI proteins from some bacteria have been shown to act as an inhibitor of DNA gyrase. Mycobacterium tuberculosis and Mycobacterium smegmatis MurI exhibit these dual characteristics. Here, we show that the two activities of M. tuberculosis MurI are unlinked and independent of each other. The racemization function of MurI is not essential for its gyrase-inhibitory property. MurI-DNA gyrase interaction influences gyrase activity but has no effect on the racemization activity of MurI. Overexpression of MurI in vivo provides resistance to the action of ciprofloxacin, suggesting the importance of the interaction in gyrase modulation. We propose that the moonlighting activity of MurI has evolved more recently than its racemase function, to play a transient yet important role in gyrase modulation.
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Affiliation(s)
- Sugopa Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Soumitra Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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32
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Fisher SL. Glutamate racemase as a target for drug discovery. Microb Biotechnol 2008; 1:345-60. [PMID: 21261855 PMCID: PMC3815242 DOI: 10.1111/j.1751-7915.2008.00031.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 01/11/2008] [Accepted: 02/15/2008] [Indexed: 11/28/2022] Open
Abstract
The bacterial cell wall is a highly cross-linked polymeric structure consisting of repeating peptidoglycan units, each of which contains a novel pentapeptide substitution which is cross-linked through transpeptidation. The incorporation of D-glutamate as the second residue is strictly conserved across the bacterial kingdom. Glutamate racemase, a member of the cofactor-independent, two-thiol-based family of amino acid racemases, has been implicated in the production and maintenance of sufficient d-glutamate pool levels required for growth. The subject of over four decades of research, it is now evident that the enzyme is conserved and essential for growth across the bacterial kingdom and has a conserved overall topology and active site architecture; however, several different mechanisms of regulation have been observed. These traits have recently been targeted in the discovery of both narrow and broad spectrum inhibitors. This review outlines the biological history of this enzyme, the recent biochemical and structural characterization of isozymes from a wide range of species and developments in the identification of inhibitors that target the enzyme as possible therapeutic agents.
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Affiliation(s)
- Stewart L Fisher
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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33
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Okrasa K, Levy C, Hauer B, Baudendistel N, Leys D, Micklefield J. Structure and Mechanism of an Unusual Malonate Decarboxylase and Related Racemases. Chemistry 2008; 14:6609-13. [DOI: 10.1002/chem.200800918] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Nakasako M, Obata R, Okubo R, Nakayama S, Miyamoto K, Ohta H. Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:610-3. [PMID: 18607088 DOI: 10.1107/s1744309108014723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 05/15/2008] [Indexed: 11/11/2022]
Abstract
Arylmalonate decarboxylase catalyses the enantioselective decarboxylation of alpha-aryl-alpha-methylmalonates to produce optically pure alpha-arylpropionates. The enzyme was crystallized with ammonium sulfate under alkaline pH conditions with the aim of understanding the mechanism of the enantioselective reaction. X-ray diffraction data collected to a resolution of 3.0 A at cryogenic temperature showed that the crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 83.13, b = 99.62, c = 139.64 A. This suggested that the asymmetric unit would contain between four and six molecules. Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process.
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Affiliation(s)
- Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522, Japan.
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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Kim KH, Bong YJ, Park JK, Shin KJ, Hwang KY, Kim EE. Structural Basis for Glutamate Racemase Inhibition. J Mol Biol 2007; 372:434-43. [PMID: 17658548 DOI: 10.1016/j.jmb.2007.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 04/19/2007] [Accepted: 05/02/2007] [Indexed: 11/24/2022]
Abstract
D-Glutamic acid is a required biosynthetic building block for peptidoglycan, and the enzyme glutamate racemase (GluR) catalyzes the inter-conversion of D and L-glutamate enantiomers. Therefore, GluR is considered as an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of GluR from Streptococcus pyogenes in both inhibitor-free and inhibitor-bound forms. The inhibitor free GluR crystallized in two different forms, which diffracted to 2.25 A and 2.5 A resolution, while the inhibitor-bound crystal diffracted to 2.5 A resolution. GluR is composed of two domains of alpha/beta protein that are related by pseudo-2-fold symmetry and the active site is located at the domain interface. The inhibitor, gamma-2-naphthylmethyl-D-glutamate, which was reported earlier as a novel potent competitive inhibitor, makes several hydrogen bonds with protein atoms, and the naphthyl moiety is located in the hydrophobic pocket. The inhibitor binding induces a disorder in one of the loops near the active site. In both crystal forms, GluR exists as a dimer and the interactions seen at the dimer interface are almost identical. This agrees well with the results from gel filtration and dynamic light-scattering studies.
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Affiliation(s)
- Kook-Han Kim
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-Dong, Sungbuk-Gu, Seoul, Korea
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Dodd D, Reese JG, Louer CR, Ballard JD, Spies MA, Blanke SR. Functional comparison of the two Bacillus anthracis glutamate racemases. J Bacteriol 2007; 189:5265-75. [PMID: 17496086 PMCID: PMC1951872 DOI: 10.1128/jb.00352-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 05/01/2007] [Indexed: 11/20/2022] Open
Abstract
Glutamate racemase activity in Bacillus anthracis is of significant interest with respect to chemotherapeutic drug design, because L-glutamate stereoisomerization to D-glutamate is predicted to be closely associated with peptidoglycan and capsule biosynthesis, which are important for growth and virulence, respectively. In contrast to most bacteria, which harbor a single glutamate racemase gene, the genomic sequence of B. anthracis predicts two genes encoding glutamate racemases, racE1 and racE2. To evaluate whether racE1 and racE2 encode functional glutamate racemases, we cloned and expressed racE1 and racE2 in Escherichia coli. Size exclusion chromatography of the two purified recombinant proteins suggested differences in their quaternary structures, as RacE1 eluted primarily as a monomer, while RacE2 demonstrated characteristics of a higher-order species. Analysis of purified recombinant RacE1 and RacE2 revealed that the two proteins catalyze the reversible stereoisomerization of L-glutamate and D-glutamate with similar, but not identical, steady-state kinetic properties. Analysis of the pH dependence of L-glutamate stereoisomerization suggested that RacE1 and RacE2 both possess two titratable active site residues important for catalysis. Moreover, directed mutagenesis of predicted active site residues resulted in complete attenuation of the enzymatic activities of both RacE1 and RacE2. Homology modeling of RacE1 and RacE2 revealed potential differences within the active site pocket that might affect the design of inhibitory pharmacophores. These results suggest that racE1 and racE2 encode functional glutamate racemases with similar, but not identical, active site features.
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Affiliation(s)
- Dylan Dodd
- Department of Microbiology, Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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May M, Mehboob S, Mulhearn DC, Wang Z, Yu H, Thatcher GR, Santarsiero BD, Johnson ME, Mesecar AD. Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design. J Mol Biol 2007; 371:1219-37. [PMID: 17610893 PMCID: PMC2736553 DOI: 10.1016/j.jmb.2007.05.093] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 05/23/2007] [Accepted: 05/29/2007] [Indexed: 12/01/2022]
Abstract
Glutamate racemase (RacE) is responsible for converting l-glutamate to d-glutamate, which is an essential component of peptidoglycan biosynthesis, and the primary constituent of the poly-gamma-d-glutamate capsule of the pathogen Bacillus anthracis. RacE enzymes are essential for bacterial growth and lack a human homolog, making them attractive targets for the design and development of antibacterial therapeutics. We have cloned, expressed and purified the two glutamate racemase isozymes, RacE1 and RacE2, from the B. anthracis genome. Through a series of steady-state kinetic studies, and based upon the ability of both RacE1 and RacE2 to catalyze the rapid formation of d-glutamate, we have determined that RacE1 and RacE2 are bona fide isozymes. The X-ray structures of B. anthracis RacE1 and RacE2, in complex with d-glutamate, were determined to resolutions of 1.75 A and 2.0 A. Both enzymes are dimers with monomers arranged in a "tail-to-tail" orientation, similar to the B. subtilis RacE structure, but differing substantially from the Aquifex pyrophilus RacE structure. The differences in quaternary structures produce differences in the active sites of racemases among the various species, which has important implications for structure-based, inhibitor design efforts within this class of enzymes. We found a Val to Ala variance at the entrance of the active site between RacE1 and RacE2, which results in the active site entrance being less sterically hindered for RacE1. Using a series of inhibitors, we show that this variance results in differences in the inhibitory activity against the two isozymes and suggest a strategy for structure-based inhibitor design to obtain broad-spectrum inhibitors for glutamate racemases.
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Affiliation(s)
- Melissa May
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
| | - Debbie C. Mulhearn
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
| | - Zhiqiang Wang
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607
| | - Huidong Yu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607
| | - Gregory R.J. Thatcher
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607
| | - Bernard D. Santarsiero
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
| | - Andrew D. Mesecar
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607
- Address correspondence to: Andrew D. Mesecar, Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago IL, 60607. Tel. 312 996-1877; Fax. 312 413-9303; E-Mail:
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Terao Y, Ijima Y, Miyamoto K, Ohta H. Inversion of enantioselectivity of arylmalonate decarboxylase via site-directed mutation based on the proposed reaction mechanism. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcatb.2006.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Sengupta S, Shah M, Nagaraja V. Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding. Nucleic Acids Res 2006; 34:5567-76. [PMID: 17020913 PMCID: PMC1635304 DOI: 10.1093/nar/gkl704] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glutamate racemase (MurI) catalyses the conversion of l-glutamate to d-glutamate, an important component of the bacterial cell wall. MurI from Escherichia coli inhibits DNA gyrase in presence of the peptidoglycan precursor. Amongst the two-glutamate racemases found in Bacillus subtilis, only one inhibits gyrase, in absence of the precursor. Mycobacterium tuberculosis has a single gene encoding glutamate racemase. Action of M.tuberculosis MurI on DNA gyrase activity has been examined and its mode of action elucidated. We demonstrate that mycobacterial MurI inhibits DNA gyrase activity, in addition to its precursor independent racemization function. The inhibition is not species-specific as E.coli gyrase is also inhibited but is enzyme-specific as topoisomerase I activity remains unaltered. The mechanism of inhibition is different from other well-known gyrase inhibitors. MurI binds to GyrA subunit of the enzyme leading to a decrease in DNA-binding of the holoenzyme. The sequestration of the gyrase by MurI results in inhibition of all reactions catalysed by DNA gyrase. MurI is thus not a typical potent inhibitor of DNA gyrase and instead its role could be in modulation of the gyrase activity.
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Affiliation(s)
- Sugopa Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of ScienceBangalore 560012, Karnataka, India
| | - Meera Shah
- Department of Microbiology and Cell Biology, Indian Institute of ScienceBangalore 560012, Karnataka, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of ScienceBangalore 560012, Karnataka, India
- Jawaharlal Nehru Centre for Advanced Scientific ResearchBangalore 560064, Karnataka, India
- To whom correspondence should be addressed. Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India. Tel: +91 80 2360 0668; Fax: +91 80 2360 2697;
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41
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Terao Y, Miyamoto K, Ohta H. Improvement of the activity of arylmalonate decarboxylase by random mutagenesis. Appl Microbiol Biotechnol 2006; 73:647-53. [PMID: 16865343 DOI: 10.1007/s00253-006-0518-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/20/2006] [Accepted: 05/23/2006] [Indexed: 11/26/2022]
Abstract
Arylmalonate decarboxylase (EC 4.1.1.76) catalyzes enantioselective decarboxylation of alpha-aryl-alpha-methylmalonates to give optically pure alpha-arylpropionates. Recently, we have succeeded in creating a double mutant enzyme that gave opposite enantionmer as the product. Unfortunately, however, the activity of the mutant decreased far lower than that of the native enzyme. Thus, we performed the directed evolution of the mutant via the random mutagenesis method employing the mutator strain Escherichia coli XL1-Red. About 50,000 mutants were screened on color assay plate, and one mutant with higher activity was obtained. Gene analysis of this mutant indicated that the obtained enzyme had an S36N mutation in addition to its original G74C/C188S mutations. The activity of the triple mutant enzyme was tenfold higher than that of the starting doubly mutated enzyme.
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Affiliation(s)
- Y Terao
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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42
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Terao Y, Miyamoto K, Ohta H. Introduction of single mutation changes arylmalonate decarboxylase to racemase. Chem Commun (Camb) 2006:3600-2. [PMID: 17047777 DOI: 10.1039/b607211a] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The introduction of only one mutation based on the estimated reaction mechanism endowed arylmalonate decarboxylase with a racemase activity, which catalyses racemisation of alpha-arylpropionates.
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Affiliation(s)
- Yosuke Terao
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
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43
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Ruzheinikov SN, Taal MA, Sedelnikova SE, Baker PJ, Rice DW. Substrate-Induced Conformational Changes in Bacillus subtilis Glutamate Racemase and Their Implications for Drug Discovery. Structure 2005; 13:1707-13. [PMID: 16271894 DOI: 10.1016/j.str.2005.07.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 07/28/2005] [Accepted: 07/29/2005] [Indexed: 11/18/2022]
Abstract
D-glutamate is an essential building block of the peptidoglycan layer in bacterial cell walls and can be synthesized from L-glutamate by glutamate racemase (RacE). The structure of a complex of B. subtilis RacE with D-glutamate reveals that the glutamate is buried in a deep pocket, whose formation at the interface of the enzyme's two domains involves a large-scale conformational rearrangement. These domains are related by pseudo-2-fold symmetry, which superimposes the two catalytic cysteine residues, which are located at equivalent positions on either side of the alpha carbon of the substrate. The structural similarity of these two domains suggests that the racemase activity of RacE arose as a result of gene duplication. The structure of the complex is dramatically different from that proposed previously and provides new insights into the RacE mechanism and an explanation for the potency of a family of RacE inhibitors, which have been developed as novel antibiotics.
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Affiliation(s)
- Sergey N Ruzheinikov
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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44
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Lee KS, Park SM, Hwang KY, Chi YM. Crystallization and preliminary X-ray crystallographic studies of glutamate racemase from Lactobacillus fermenti. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:199-201. [PMID: 16510993 PMCID: PMC1952270 DOI: 10.1107/s1744309104034426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Accepted: 12/29/2004] [Indexed: 11/10/2022]
Abstract
Glutamate racemase catalyzes the conversion of L-glutamic acid to D-glutamic acid and vice versa. Since D-glutamic acid is one of the essential amino acids present in peptidoglycan, glutamate racemase has been considered to be an attractive target for the design of new antibacterial drugs. Glutamate racemase from Lactobacillus fermenti has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 8000 as a precipitant. The crystals belong to the orthorhombic space group C222(1), with unit-cell parameters a = 98.32, b = 184.09, c = 45.99 A. The asymmetric unit contains one molecule, corresponding to a VM value of 1.84 A3 Da(-1). A complete data set has been collected from the native enzyme at 2.28 A resolution using a synchrotron-radiation source.
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Affiliation(s)
- Ki-Seog Lee
- Division of Biotechnology and Genetic Engineering, Korea University, Seoul 136-701, South Korea
| | - Seon-Mi Park
- Division of Biotechnology and Genetic Engineering, Korea University, Seoul 136-701, South Korea
| | - Kwang Yeon Hwang
- Biomedical Research Center, Division of Life Science, Korea Institute of Science and Technology, 39-1 Hawolgok-dong Seongbuk-gu, Seoul 136-791, South Korea
- Correspondence e-mail: ,
| | - Young-Min Chi
- Division of Biotechnology and Genetic Engineering, Korea University, Seoul 136-701, South Korea
- Correspondence e-mail: ,
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Abstract
Pyridoxal phosphate (PLP)-dependent enzymes are unrivaled in the diversity of reactions that they catalyze. New structural data have paved the way for targeted mutagenesis and mechanistic studies and have provided a framework for interpretation of those results. Together, these complementary approaches yield new insight into function, particularly in understanding the origins of substrate and reaction type specificity. The combination of new sequences and structures enables better reconstruction of their evolutionary heritage and illuminates unrecognized similarities within this diverse group of enzymes. The important metabolic roles of many PLP-dependent enzymes drive efforts to design specific inhibitors, which are now guided by the availability of comprehensive structural and functional databases. Better understanding of the function of this important group of enzymes is crucial not only for inhibitor design, but also for the design of improved protein-based catalysts.
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Affiliation(s)
- Andrew C Eliot
- Department of Chemistry University of California, Berkeley, California 94720-3206, USA.
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46
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Matoishi K, Ueda M, Miyamoto K, Ohta H. Mechanism of asymmetric decarboxylation of α-aryl-α-methylmalonate catalyzed by arylmalonate decarboxylase originated from Alcaligenes bronchisepticus. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2003.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Watanabe A, Yamaguchi S, Urabe K, Asada Y. Occurrence of a unique amino acid racemase in a basidiomycetous mushroom, Lentinus edodes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(03)00102-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Application of a thermostable glutamate racemase from Bacillus sp. SK-1 for the production of d-phenylalanine in a multi-enzyme system. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1381-1177(02)00011-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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49
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Christen P, Mehta PK. From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes. CHEM REC 2002; 1:436-47. [PMID: 11933250 DOI: 10.1002/tcr.10005] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The pyridoxal-5'-phosphate (vitamin B(6))-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. Thus, the common mechanistic features of B(6) enzymes are not accidental historical traits but reflect evolutionary or chemical necessities. The B(6) enzymes belong to four independent evolutionary lineages of paralogous proteins, of which the alpha family (with aspartate aminotransferase as the prototype enzyme) is by far the largest and most diverse. The considerably smaller beta family (tryptophan synthase beta as the prototype enzyme) is structurally and functionally more homogenous. Both the D-alanine aminotransferase family and the alanine racemase family consist of only a few enzymes. The primordial pyridoxal-5'-phosphate-dependent protein catalysts apparently first diverged into reaction-specific protoenzymes, which then diverged further by specializing for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages, providing examples of convergent enzyme evolution. The functional specialization of most B(6) enzymes seems to have already occurred in the universal ancestor cell before the divergence of eukaryotes, archebacteria, and eubacteria 1500 million years ago. Pyridoxal-5'-phosphate must have emerged very early in biological evolution; conceivably, metal ions and organic cofactors were the first biological catalysts. To simulate particular steps of molecular evolution, both the substrate and reaction specificity of existent B(6) enzymes were changed by substitution of active-site residues, and monoclonal pyridoxal-5'-phosphate-dependent catalytic antibodies were produced with selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.
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Affiliation(s)
- P Christen
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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