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Rothe P, Wamp S, Rosemeyer L, Rismondo J, Doellinger J, Gründling A, Halbedel S. Cytosolic Factors Controlling PASTA Kinase-Dependent ReoM Phosphorylation. Mol Microbiol 2024; 122:514-533. [PMID: 39245639 DOI: 10.1111/mmi.15307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024]
Abstract
Bacteria adapt the biosynthesis of their envelopes to specific growth conditions and prevailing stress factors. Peptidoglycan (PG) is the major component of the cell wall in Gram-positive bacteria, where PASTA kinases play a central role in PG biosynthesis regulation. Despite their importance for growth, cell division and antibiotic resistance, the mechanisms of PASTA kinase activation are not fully understood. ReoM, a recently discovered cytosolic phosphoprotein, is one of the main substrates of the PASTA kinase PrkA in the Gram-positive human pathogen Listeria monocytogenes. Depending on its phosphorylation, ReoM controls proteolytic stability of MurA, the first enzyme in the PG biosynthesis pathway. The late cell division protein GpsB has been implicated in PASTA kinase signalling. Consistently, we show that L. monocytogenes prkA and gpsB mutants phenocopied each other. Analysis of in vivo ReoM phosphorylation confirmed GpsB as an activator of PrkA leading to the description of structural features in GpsB that are important for kinase activation. We further show that ReoM phosphorylation is growth phase-dependent and that this kinetic is reliant on the protein phosphatase PrpC. ReoM phosphorylation was inhibited in mutants with defects in MurA degradation, leading to the discovery that MurA overexpression prevented ReoM phosphorylation. Overexpressed MurA must be able to bind its substrates and interact with ReoM to exert this effect, but the extracellular PASTA domains of PrkA or MurJ flippases were not required. Our results indicate that intracellular signals control ReoM phosphorylation and extend current models describing the mechanisms of PASTA kinase activation.
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Affiliation(s)
- Patricia Rothe
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Lisa Rosemeyer
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Jeanine Rismondo
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Joerg Doellinger
- ZBS6 - Proteomics and Spectroscopy, Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Angelika Gründling
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
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Yang Y, Tan L, He S, Hao B, Huang X, Zhou Y, Shang W, Peng H, Hu Z, Ding R, Rao X. Sub-MIC vancomycin enhances the antibiotic tolerance of vancomycin-intermediate Staphylococcus aureus through downregulation of protein succinylation. Microbiol Res 2024; 282:127635. [PMID: 38340572 DOI: 10.1016/j.micres.2024.127635] [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] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Bacteria develop tolerance after transient exposure to antibiotics, and tolerance is a significant driver of resistance. The purpose of this study is to evaluate the mechanisms underlying tolerance formation in vancomycin-intermediate Staphylococcus aureus (VISA) strains. VISA strains were cultured with sub-minimum inhibitory concentrations (sub-MICs) of vancomycin. Enhanced vancomycin tolerance was observed in VISA strains with distinct genetic lineages. Western blot revealed that the VISA protein succinylation (Ksucc) levels decreased with the increase in vancomycin exposure. Importantly, Ksucc modification, vancomycin tolerance, and cell wall synthesis were simultaneously affected after deletion of SacobB, which encodes a desuccinylase in S. aureus. Several Ksucc sites were identified in MurA, and vancomycin MIC levels of murA mutant and Ksucc-simulated (MurA(K69E) and MurA(K191E)) mutants were reduced. The vancomycin MIC levels of K65-MurA(K191E) in particular decreased to 1 mg/L, converting VISA strain K65 to a vancomycin-susceptible S. aureus strain. We further demonstrated that the enzymatic activity of MurA was dependent on Ksucc modification. Our data suggested the influence of vancomycin exposure on bacterial tolerance, and protein Ksucc modification is a novel mechanism in regulating vancomycin tolerance.
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Affiliation(s)
- Yi Yang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Li Tan
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Siyuan He
- College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Bo Hao
- College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiaonan Huang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yumin Zhou
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Huagang Peng
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhen Hu
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Ruolan Ding
- Department of Microbiology, School of Medicine, Chongqing University, Chongqing 400044, China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Key Laboratory of Microbial Engineering Under the Educational Committee in Chongqing, Army Medical University (Third Military Medical University), Chongqing 400038, China.
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Boulhissa I, Chikhi A, Bensegueni A, Ghattas MA, Mokrani EH, Alrawashdeh S, Obaid DEE. Investigation of New Inhibitors of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) by Virtual Screening with Antibacterial Assessment. Curr Comput Aided Drug Des 2021; 17:214-224. [PMID: 32053077 DOI: 10.2174/1573409916666200213124929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Considering the interesting role in the peptidoglycan biosynthesis pathway, the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase is an attractive target to develop new antibacterial agents. It catalyzes the first key step of this pathway and its inhibition leads to bacterial cell death. Fosfomycin is known as the natural inhibitor of MurA. OBJECTIVE The study aimed to introduce new inhibitors of MurA by virtual screening of different chemical compounds libraries, and test the best scored "virtual hits" against three pathogenic bacteria: Escherichia coli, Bacillus subtilis and Staphylococcus aureus. METHODS A virtual screening of the structural analogues of fosfomycin downloaded from the Pub- Chem database was performed. Moreover, French National Chemical Library and ZINC database were also utilized to identify new structures different from fosfomycin. FlexX was the software used for this study. The antibacterial testing was divided into two methods: disk diffusion and broth dilution. RESULTS A set of virtual hits was found to have better energy score than that of fosfomycin, seven of them were tested in vitro. In addition, the disk diffusion method explored four compounds that exhibited antibacterial activity: CID-21680357 (fosfomycin analogue), AB-00005001, ZINC04658565, and ZINC901335. The testing was continued by broth dilution method for both compounds CID-21680357 and ZINC901335 to determine their minimum inhibitory concentrations, and ZINC901335 had the best value with 457μg/ml against Staphylococcus aureus. CONCLUSION Four compounds were found and proven in silico and in vitro to have antibacterial activity, namely CID-21680357, AB-00005001, ZINC04658565, and ZINC901335.
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Affiliation(s)
- Ilham Boulhissa
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
| | - El H Mokrani
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Sara Alrawashdeh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
| | - Dana E E Obaid
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
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Mihalovits LM, Ferenczy GG, Keserű GM. Catalytic Mechanism and Covalent Inhibition of UDP- N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials. J Chem Inf Model 2019; 59:5161-5173. [PMID: 31715096 DOI: 10.1021/acs.jcim.9b00691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) catalyzes the first step in the biosynthesis of the bacterial cell wall. This pathway is essential for the growth of bacteria but missing in mammals, that nominates MurA as an attractive antibacterial target. MurA has a flexible loop whose conformational change is known to be part of the activation mechanism of the enzyme. We have shown that the loop closed conformation makes the proton transfer from Cys115 to His394 possible by a low barrier exothermic process. QM/MM MD simulations revealed that the activated thiolate is able to react with phosphoenolpyruvate (PEP), the natural substrate of MurA. The binding free energy profile of several covalent inhibitors with various warheads reacting with the activated Cys115 was calculated by QM/MM MD simulations and confirmed that reaction barrier heights tend to separate active from inactive compounds. Our results give new insight into the catalytic mechanism and covalent inhibition of MurA and suggest that QM/MM MD simulations are able to support ligand design by providing sensible relative free energy barriers for covalent inhibitors with various warheads reacting with thiolate nucleophiles.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
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Mondal SI, Mahmud Z, Elahi M, Akter A, Jewel NA, Muzahidul Islam M, Ferdous S, Kikuchi T. Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. In Silico Pharmacol 2017; 5:1. [PMID: 28401513 DOI: 10.1007/s40203-017-0021-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/20/2017] [Indexed: 11/29/2022] Open
Abstract
Protein-protein interaction (PPI) and host-pathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections. In this research, we attempted to identify new drug target based on PPI and HPI computation approaches and subsequently design new drug against devastating enterohemorrhagic Escherichia coli O104:H4 C277-11 (Broad), which causes life-threatening food borne disease outbreak in Germany and other countries in Europe in 2011. Our systematic in silico analysis on PPI and HPI of E. coli O104:H4 was able to identify bacterial D-galactose-binding periplasmic and UDP-N-acetylglucosamine 1-carboxyvinyltransferase as attractive candidates for new drug targets. Furthermore, computational three-dimensional structure modeling and subsequent molecular docking finally proposed [3-(5-Amino-7-Hydroxy-[1,2,3]Triazolo[4,5-D]Pyrimidin-2-Yl)-N-(3,5-Dichlorobenzyl)-Benzamide)] and (6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one) as promising candidate drugs for further evaluation and development for E. coli O104:H4 mediated diseases. Identification of new drug target would be of great utility for humanity as the demand for designing new drugs to fight infections is increasing due to the developing resistance and side effects of current treatments. This research provided the basis for computer aided drug design which might be useful for new drug target identification and subsequent drug design for other infectious organisms.
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Affiliation(s)
- Shakhinur Islam Mondal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh. .,Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Zabed Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Montasir Elahi
- Department of Diagnosis, Prevention and Treatment of Dementia, Juntendo University Graduate School of Medicine, Bunkyō, Tokyo, Japan
| | - Arzuba Akter
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.,Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Sabiha Ferdous
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
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6
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Sonkar A, Shukla H, Shukla R, Kalita J, Pandey T, Tripathi T. UDP-N-Acetylglucosamine enolpyruvyl transferase (MurA) of Acinetobacter baumannii (AbMurA): Structural and functional properties. Int J Biol Macromol 2017; 97:106-114. [DOI: 10.1016/j.ijbiomac.2016.12.082] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/23/2016] [Accepted: 12/31/2016] [Indexed: 01/02/2023]
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7
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Lima AH, dos Santos AM, Alves CN, Lameira J. Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme fromPseudomonas aeruginosa. Chem Biol Drug Des 2016; 89:599-607. [DOI: 10.1111/cbdd.12882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/16/2016] [Accepted: 09/29/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos; Instituto de Ciências Exatas e Naturais; Universidade Federal do Pará; Belém PA Brasil
| | - Alberto M. dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos; Instituto de Ciências Exatas e Naturais; Universidade Federal do Pará; Belém PA Brasil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos; Instituto de Ciências Exatas e Naturais; Universidade Federal do Pará; Belém PA Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos; Instituto de Ciências Exatas e Naturais; Universidade Federal do Pará; Belém PA Brasil
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8
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Cloning, expression and characterization of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from Wolbachia endosymbiont of human lymphatic filarial parasite Brugia malayi. PLoS One 2014; 9:e99884. [PMID: 24941309 PMCID: PMC4062475 DOI: 10.1371/journal.pone.0099884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/19/2014] [Indexed: 12/21/2022] Open
Abstract
Wolbachia, an endosymbiont of filarial nematode, is considered a promising target for treatment of lymphatic filariasis. Although functional characterization of the Wolbachia peptidoglycan assembly has not been fully explored, the Wolbachia genome provides evidence for coding all of the genes involved in lipid II biosynthesis, a part of peptidoglycan biosynthesis pathway. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is one of the lipid II biosynthesis pathway enzymes and it has inevitably been recognized as an antibiotic target. In view of the vital role of MurA in bacterial viability and survival, MurA ortholog from Wolbachia endosymbiont of Brugia malayi (wBm-MurA) was cloned, expressed and purified for further molecular characterization. The enzyme kinetics and inhibition studies were undertaken using fosfomycin. wBm-MurA was found to be expressed in all the major life stages of B. malayi and was immunolocalized in Wolbachia within the microfilariae and female adults by the confocal microscopy. Sequence analysis suggests that the amino acids crucial for enzymatic activity are conserved. The purified wBm-MurA was shown to possess the EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) like activity at a broad pH range with optimal activity at pH 7.5 and 37°C temperature. The apparent affinity constant (Km) for the substrate UDP-N-acetylglucosamine was found to be 0.03149 mM and for phosphoenolpyruvate 0.009198 mM. The relative enzymatic activity was inhibited ∼2 fold in presence of fosfomycin. Superimposition of the wBm-MurA homology model with the structural model of Haemophilus influenzae (Hi-MurA) suggests binding of fosfomycin at the same active site. The findings suggest wBm-MurA to be a putative antifilarial drug target for screening of novel compounds.
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Oberdorfer G, Binter A, Ginj C, Macheroux P, Gruber K. Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis. J Biol Chem 2012; 287:31427-36. [PMID: 22810238 DOI: 10.1074/jbc.m112.352096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nikkomycins are peptide-nucleoside compounds with fungicidal, acaricidal, and insecticidal properties because of their strong inhibition of chitin synthase. Thus, they are potential antibiotics especially for the treatment of immunosuppressed patients, for those undergoing chemotherapy, or after organ transplants. Although their chemical structure has been known for more than 30 years, only little is known about their complex biosynthesis. The genes encoding for proteins involved in the biosynthesis of the nucleoside moiety of nikkomycins are co-transcribed in the same operon, comprising the genes nikIJKLMNO. The gene product NikO was shown to belong to the family of enolpyruvyl transferases and to catalyze the transfer of an enolpyruvyl moiety from phosphoenolpyruvate to the 3'-hydroxyl group of UMP. Here, we report activity and inhibition studies of the wild-type enzyme and the variants C130A and D342A. The x-ray crystal structure revealed differences between NikO and its homologs. Furthermore, our studies led to conclusions concerning substrate binding and preference as well as to conclusions about inhibition/alkylation by the antibiotic fosfomycin.
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Affiliation(s)
- Gustav Oberdorfer
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
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10
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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11
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Zhu JY, Yang Y, Han H, Betzi S, Olesen SH, Marsilio F, Schönbrunn E. Functional consequence of covalent reaction of phosphoenolpyruvate with UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA). J Biol Chem 2012; 287:12657-67. [PMID: 22378791 PMCID: PMC3339971 DOI: 10.1074/jbc.m112.342725] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/27/2012] [Indexed: 11/06/2022] Open
Abstract
The enzyme MurA has been an established antibiotic target since the discovery of fosfomycin, which specifically inhibits MurA by covalent modification of the active site residue Cys-115. Early biochemical studies established that Cys-115 also covalently reacts with substrate phosphoenolpyruvate (PEP) to yield a phospholactoyl adduct, but the structural and functional consequences of this reaction remained obscure. We captured and depicted the Cys-115-PEP adduct of Enterobacter cloacae MurA in various reaction states by X-ray crystallography. The data suggest that cellular MurA predominantly exists in a tightly locked complex with UDP-N-acetylmuramic acid (UNAM), the product of the MurB reaction, with PEP covalently attached to Cys-115. The uniqueness and rigidity of this "dormant" complex was previously not recognized and presumably accounts for the failure of drug discovery efforts toward the identification of novel and effective MurA inhibitors. We demonstrate that recently published crystal structures of MurA from various organisms determined by different laboratories were indeed misinterpreted and actually contain UNAM and covalently bound PEP. The Cys-115-PEP adduct was also captured in vitro during the reaction of free MurA and substrate UDP-N-acetylglucosamine or isomer UDP-N-acetylgalactosamine. The now available series of crystal structures allows a comprehensive view of the reaction cycle of MurA. It appears that the covalent reaction of MurA with PEP fulfills dual functions by tightening the complex with UNAM for the efficient feedback regulation of murein biosynthesis and by priming the PEP molecule for instantaneous reaction with substrate UDP-N-acetylglucosamine.
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Affiliation(s)
- Jin-Yi Zhu
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Yan Yang
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Huijong Han
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Stephane Betzi
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Sanne H. Olesen
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Frank Marsilio
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Ernst Schönbrunn
- From the Drug Discovery Department, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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12
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Gautam A, Rishi P, Tewari R. UDP-N-acetylglucosamine enolpyruvyl transferase as a potential target for antibacterial chemotherapy: recent developments. Appl Microbiol Biotechnol 2011; 92:211-25. [PMID: 21822642 DOI: 10.1007/s00253-011-3512-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 07/17/2011] [Accepted: 07/24/2011] [Indexed: 11/24/2022]
Abstract
The emergence of antibiotic resistance in bacterial pathogens has foxed the health organizations which are actively scrambling for solutions. The available data indicate an increased morbidity in infections often leading to mortality among patients where drug-resistant pathogens have negated the effect of the medicines. In the context of developing "novel bacterial inhibitors" for killing or arresting the growth of drug-resistant pathogens, UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an enzyme that provides hope for the future. This enzyme catalyzes the first committed step in the biosynthesis of peptidoglycan, an integral and essential component of the bacterial cell wall. MurA enzyme is neither present nor required by mammals and shows poor homology with human proteins. Therefore, it is an ideal target for antibacterial chemotherapy. Till date, 18 structures of MurA (in native and ligand-bound forms) from different bacterial pathogens have been solved. In the last 2 years, eight structures of bacterial MurA have been submitted to the Protein Data Bank and many inhibitors discovered. The present review discusses the structural and functional features of MurA of bacterial pathogens along with the development of MurA-targeted inhibitors.
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Affiliation(s)
- Ankur Gautam
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh 160036, India
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13
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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14
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Berti PJ, Chindemi P. Catalytic residues and an electrostatic sandwich that promote enolpyruvyl shikimate 3-phosphate synthase (AroA) catalysis. Biochemistry 2009; 48:3699-707. [PMID: 19271774 DOI: 10.1021/bi802251s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enolpyruvylshikimate 3-phosphate synthase (EPSP synthase, AroA) catalyzes the sixth step in aromatic amino acid biosynthesis. It forms EPSP from shikimate 3-phosphate (S3P) and phosphoenolpyruvate (PEP) in an addition/elimination reaction that proceeds through a tetrahedral intermediate. In spite of numerous mechanistic studies, the catalytic roles of specific amino acid residues remain an open question. Recent experimental evidence for cationic intermediates or cationic transition states, and a consideration of the catalytic imperative, have guided this study on the catalytic roles of Lys22 (K22), Asp313 (D313), and Glu341 (E341). Steady-state and pre-steady-state kinetics and protein stability studies showed that mutations of D313 and E341 caused k(cat) to decrease up to 30,000-fold and 76,000-fold, respectively, while the effects on K(M) were modest, never more than 40-fold. Thus, both are identified as catalytic residues. In an active site that is overwhelmingly positively charged, the D313 and E341 side chains are positioned to form an "electrostatic sandwich" around the positive charge at C2 in cationic intermediates/transition states, stabilizing them and thereby promoting catalysis. Mutation of K22 showed large effects on K(M,S3P) (100-fold), K(M,PEP) (>760-fold), and up to 120-fold on k(cat). Thus, K22 had roles in both substrate-binding and transition-state stabilization. These results support the identification of E341 and K22 as general acid/base catalytic residues.
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Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
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Steinbach A, Scheidig AJ, Klein CD. The unusual binding mode of cnicin to the antibacterial target enzyme MurA revealed by X-ray crystallography. J Med Chem 2008; 51:5143-7. [PMID: 18672863 DOI: 10.1021/jm800609p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the X-ray structure of the antibacterial target enzyme MurA in complex with its substrate UNAG and the sesquiterpene lactone cnicin, a potent inhibitor of the enzyme. The structure reveals that MurA has catalyzed the formation of a covalent adduct between cnicin and UNAG. This adduct, which can be regarded as a noncovalent suicide inhibitor, has been formed by an unusual "anti-Michael" 1,3-addition of UNAG to an alpha,beta-unsaturated carbonyl function in cnicin.
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Affiliation(s)
- Anke Steinbach
- Pharmazeutische Chemie, Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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Comparison of the essential cellular functions of the two murA genes of Bacillus anthracis. Antimicrob Agents Chemother 2008; 52:2009-13. [PMID: 18378720 DOI: 10.1128/aac.01594-07] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeted antisense and gene replacement mutagenesis experiments demonstrate that only the murA1 gene and not the murA2 gene is required for the normal cellular growth of Bacillus anthracis. Antisense-based modulation of murA1 gene expression hypersensitizes cells to the MurA-specific antibiotic fosfomycin despite the normally high resistance of B. anthracis to this drug.
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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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McCoy AJ, Maurelli AT. Building the invisible wall: updating the chlamydial peptidoglycan anomaly. Trends Microbiol 2006; 14:70-7. [PMID: 16413190 DOI: 10.1016/j.tim.2005.12.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 11/25/2005] [Accepted: 12/20/2005] [Indexed: 11/22/2022]
Abstract
The existence of peptidoglycan (PG) in chlamydiae has long been debated. Genome sequencing of members of the Chlamydiaceae family and Protochlamydia amoebophila has uncovered a nearly complete pathway for PG synthesis in these organisms. The recent use of microarray and proteomic analysis methods has revealed that PG synthesis genes are expressed primarily during reticulate body development and division. Furthermore, key genes in the chlamydial PG synthesis pathway encode functional PG synthesis enzymes, some of which provide the basis for the susceptibility of chlamydiae to PG inhibitors. Recent studies shed light on how the construction of a cell wall in chlamydiae is taking shape and why the wall is being built.
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Affiliation(s)
- Andrea J McCoy
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA
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Thomas AM, Ginj C, Jelesarov I, Amrhein N, Macheroux P. Role of K22 and R120 in the covalent binding of the antibiotic fosfomycin and the substrate-induced conformational change in UDP-N-acetylglucosamine enolpyruvyl transferase. ACTA ACUST UNITED AC 2004; 271:2682-90. [PMID: 15206933 DOI: 10.1111/j.1432-1033.2004.04196.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), catalyzes the first step in the biosynthesis of peptidoglycan, involving the transfer of the intact enolpyruvyl moiety from phosphoenolpyruvate to the 3'-hydroxyl group of UDP-N-acetylglucosamine (UDPNAG). The enzyme is irreversibly inhibited by the antibiotic fosfomycin. The inactivation is caused by alkylation of a highly conserved cysteine residue (C115) that participates in the binding of phosphoenolpyruvate. The three-dimensional structure of the enzyme suggests that two residues may play a decisive role in fosfomycin binding: K22 and R120. To investigate the role of these residues, we have generated the K22V, K22E, K22R and R120K single mutant proteins as well as the K22V/R120K and K22V/R120V double mutant proteins. We demonstrated that the K22R mutant protein behaves similarly to wild-type enzyme, whereas the K22E mutant protein failed to form the covalent adduct. On the other hand, the K22V mutant protein requires the presence of UDPNAG for the formation of the adduct indicating that UDPNAG plays a crucial role in the organization of productive interactions in the active site. This model receives strong support from heat capacity changes observed for the K22V/R120K and R120K mutant proteins: in both mutant proteins, the heat capacity changes are markedly reduced indicating that their ability to form a closed protein conformation is impeded due to the R120K exchange.
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Affiliation(s)
- Alison M Thomas
- Eidgenössische Technische Hochschule Zürich, Institute of Plant Sciences, Department of Agricultural and Food Sciences and Department of Biology, Zürich, Switzerland
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El Zoeiby A, Sanschagrin F, Levesque RC. Structure and function of the Mur enzymes: development of novel inhibitors. Mol Microbiol 2003; 47:1-12. [PMID: 12492849 DOI: 10.1046/j.1365-2958.2003.03289.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One of the biggest challenges for recent medical research is the continuous development of new antibiotics interacting with bacterial essential mechanisms. The machinery for peptidoglycan biosynthesis is a rich source of crucial targets for antibacterial chemotherapy. The cytoplasmic steps of the biosynthesis of peptidoglycan precursor, catalysed by a series of Mur enzymes, are excellent candidates for drug development. There has been growing interest in these bacterial enzymes over the last decade. Many studies attempted to understand the detailed mechanisms and structural features of the key enzymes MurA to MurF. Only MurA is inhibited by a known antibiotic, fosfomycin. Several attempts made to develop novel inhibitors of this pathway are discussed in this review. Three novel inhibitors of MurA were identified recently. 4-Thiazolidinone compounds were designed as MurB inhibitors. Many phosphinic acid derivatives and substrate analogues were identified as inhibitors of the MurC to MurF amino acid ligases.
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Affiliation(s)
- Ahmed El Zoeiby
- Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculté de Médecine, Pavillon Charles-Eugène Marchand, Université Laval, Ste-Foy, Québec, Canada, G1K 7P4
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