1uae Citations

Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin.

Abstract

Background

UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), catalyses the first committed step of bacterial cell wall biosynthesis and is a target for the antibiotic fosfomycin. The only other known enolpyruvyl transferase is 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, an enzyme involved in the shikimic acid pathway and the target for the herbicide glyphosate. Inhibitors of enolpyruvyl transferases are of biotechnological interest as MurA and EPSP synthase are found exclusively in plants and microbes.

Results

The crystal structure of Escherichia coli MurA complexed with UDP-N-acetylglucosamine (UDP-GlcNAc) and fosfomycin has been determined at 1.8 A resolution. The structure consists of two domains with the active site located between them. The domains have a very similar secondary structure, and the overall protein architecture is similar to that of EPSP synthase. The fosfomycin molecule is covalently bound to the cysteine residue Cys115, whereas UDP-GlcNAc makes several hydrogen-bonding interactions with residues from both domains.

Conclusion

The present structure reveals the mode of binding of the natural substrate UDP-GlcNAc and of the drug fosfomycin, and provides information on the residues involved in catalysis. These results should aid the design of inhibitors which would interfere with enzyme-catalyzed reactions in the early stage of the bacterial cell wall biosynthesis. Furthermore, the crystal structure of MurA provides a model for predicting active-site residues in EPSP synthase that may be involved in catalysis and substrate binding.

Reviews - 1uae mentioned but not cited (1)

  1. Modeling enzyme-ligand binding in drug discovery. Konc J, Lešnik S, Janežič D. J Cheminform 7 48 (2015)

Articles - 1uae mentioned but not cited (5)

  1. A graph-theory algorithm for rapid protein side-chain prediction. Canutescu AA, Shelenkov AA, Dunbrack RL. Protein Sci. 12 2001-2014 (2003)
  2. Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. Petrova NV, Wu CH. BMC Bioinformatics 7 312 (2006)
  3. Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Dima RI, Thirumalai D. Biophys. J. 83 1268-1280 (2002)
  4. Predicting protein function from structure: unique structural features of proteases. Stawiski EW, Baucom AE, Lohr SC, Gregoret LM. Proc. Natl. Acad. Sci. U.S.A. 97 3954-3958 (2000)
  5. Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin. Bensen DC, Rodriguez S, Nix J, Cunningham ML, Tari LW. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 382-385 (2012)


Reviews citing this publication (15)

  1. Fosfomycin: Mechanism and Resistance. Silver LL. Cold Spring Harb Perspect Med 7 (2017)
  2. Covalent inhibitors design and discovery. De Cesco S, Kurian J, Dufresne C, Mittermaier AK, Moitessier N. Eur J Med Chem 138 96-114 (2017)
  3. Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. Moraes GL, Gomes GC, Monteiro de Sousa PR, Alves CN, Govender T, Kruger HG, Maguire GE, Lamichhane G, Lameira J. Tuberculosis (Edinb) 95 95-111 (2015)
  4. Fosfomycin: evaluation of the published evidence on the emergence of antimicrobial resistance in Gram-negative pathogens. Karageorgopoulos DE, Wang R, Yu XH, Falagas ME. J. Antimicrob. Chemother. 67 255-268 (2012)
  5. The structural biology of enzymes involved in natural product glycosylation. Singh S, Phillips GN, Thorson JS. Nat Prod Rep 29 1201-1237 (2012)
  6. Structural perspective of peptidoglycan biosynthesis and assembly. Lovering AL, Safadi SS, Strynadka NC. Annu. Rev. Biochem. 81 451-478 (2012)
  7. Electrophilic natural products and their biological targets. Gersch M, Kreuzer J, Sieber SA. Nat Prod Rep 29 659-682 (2012)
  8. Biosynthesis of phosphonic and phosphinic acid natural products. Metcalf WW, van der Donk WA. Annu. Rev. Biochem. 78 65-94 (2009)
  9. Clinical significance of the pharmacokinetic and pharmacodynamic characteristics of fosfomycin for the treatment of patients with systemic infections. Roussos N, Karageorgopoulos DE, Samonis G, Falagas ME. Int. J. Antimicrob. Agents 34 506-515 (2009)
  10. Cytoplasmic steps of peptidoglycan biosynthesis. Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. FEMS Microbiol. Rev. 32 168-207 (2008)
  11. Structure, function and dynamics in the mur family of bacterial cell wall ligases. Smith CA. J. Mol. Biol. 362 640-655 (2006)
  12. The structural basis of substrate translocation by the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Lemieux MJ, Huang Y, Wang DN. Curr. Opin. Struct. Biol. 14 405-412 (2004)
  13. Glycerol-3-phosphate transporter of Escherichia coli: structure, function and regulation. Lemieux MJ, Huang Y, Wang DN. Res. Microbiol. 155 623-629 (2004)
  14. Structure and function of the Mur enzymes: development of novel inhibitors. El Zoeiby A, Sanschagrin F, Levesque RC. Mol. Microbiol. 47 1-12 (2003)
  15. The bacterial cell wall as a source of antibacterial targets. Green DW. Expert Opin. Ther. Targets 6 1-19 (2002)

Articles citing this publication (40)

  1. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Svergun DI. Biophys. J. 76 2879-2886 (1999)
  2. The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis. Ha S, Walker D, Shi Y, Walker S. Protein Sci. 9 1045-1052 (2000)
  3. FosB, a cysteine-dependent fosfomycin resistance protein under the control of sigma(W), an extracytoplasmic-function sigma factor in Bacillus subtilis. Cao M, Bernat BA, Wang Z, Armstrong RN, Helmann JD. J. Bacteriol. 183 2380-2383 (2001)
  4. Conformational changes observed in enzyme crystal structures upon substrate binding. Gutteridge A, Thornton J. J. Mol. Biol. 346 21-28 (2005)
  5. Structural basis for the interaction of the fluorescence probe 8-anilino-1-naphthalene sulfonate (ANS) with the antibiotic target MurA. Schonbrunn E, Eschenburg S, Luger K, Kabsch W, Amrhein N. Proc. Natl. Acad. Sci. U.S.A. 97 6345-6349 (2000)
  6. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O. EMBO J. 16 3416-3425 (1997)
  7. Molecular mechanisms of fosfomycin resistance in clinical isolates of Escherichia coli. Takahata S, Ida T, Hiraishi T, Sakakibara S, Maebashi K, Terada S, Muratani T, Matsumoto T, Nakahama C, Tomono K. Int. J. Antimicrob. Agents 35 333-337 (2010)
  8. Identification and characterization of new inhibitors of the Escherichia coli MurA enzyme. Baum EZ, Montenegro DA, Licata L, Turchi I, Webb GC, Foleno BD, Bush K. Antimicrob. Agents Chemother. 45 3182-3188 (2001)
  9. Two active forms of UDP-N-acetylglucosamine enolpyruvyl transferase in gram-positive bacteria. Du W, Brown JR, Sylvester DR, Huang J, Chalker AF, So CY, Holmes DJ, Payne DJ, Wallis NG. J. Bacteriol. 182 4146-4152 (2000)
  10. Heterologous production of fosfomycin and identification of the minimal biosynthetic gene cluster. Woodyer RD, Shao Z, Thomas PM, Kelleher NL, Blodgett JA, Metcalf WW, van der Donk WA, Zhao H. Chem. Biol. 13 1171-1182 (2006)
  11. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Schwartz R, Istrail S, King J. Protein Sci. 10 1023-1031 (2001)
  12. Synergy of fosfomycin with carbapenems, colistin, netilmicin, and tigecycline against multidrug-resistant Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa clinical isolates. Samonis G, Maraki S, Karageorgopoulos DE, Vouloumanou EK, Falagas ME. Eur. J. Clin. Microbiol. Infect. Dis. 31 695-701 (2012)
  13. The nature of Staphylococcus aureus MurA and MurZ and approaches for detection of peptidoglycan biosynthesis inhibitors. Blake KL, O'Neill AJ, Mengin-Lecreulx D, Henderson PJ, Bostock JM, Dunsmore CJ, Simmons KJ, Fishwick CW, Leeds JA, Chopra I. Mol. Microbiol. 72 335-343 (2009)
  14. Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors. Babajan B, Chaitanya M, Rajsekhar C, Gowsia D, Madhusudhana P, Naveen M, Chitta SK, Anuradha CM. Interdiscip Sci 3 204-216 (2011)
  15. Pharmacodynamics of fosfomycin: insights into clinical use for antimicrobial resistance. Docobo-Pérez F, Drusano GL, Johnson A, Goodwin J, Whalley S, Ramos-Martín V, Ballestero-Tellez M, Rodriguez-Martinez JM, Conejo MC, van Guilder M, Rodríguez-Baño J, Pascual A, Hope WW. Antimicrob. Agents Chemother. 59 5602-5610 (2015)
  16. Heteroresistance to fosfomycin is predominant in Streptococcus pneumoniae and depends on the murA1 gene. Engel H, Gutiérrez-Fernández J, Flückiger C, Martínez-Ripoll M, Mühlemann K, Hermoso JA, Hilty M, Hathaway LJ. Antimicrob. Agents Chemother. 57 2801-2808 (2013)
  17. Comparison of the essential cellular functions of the two murA genes of Bacillus anthracis. Kedar GC, Brown-Driver V, Reyes DR, Hilgers MT, Stidham MA, Shaw KJ, Finn J, Haselbeck RJ. Antimicrob. Agents Chemother. 52 2009-2013 (2008)
  18. Staphylococcal Drp35 is the functional counterpart of the eukaryotic PONs. Morikawa K, Hidaka T, Murakami H, Hayashi H, Ohta T. FEMS Microbiol. Lett. 249 185-190 (2005)
  19. Identification of druggable targets for Acinetobacter baumannii via subtractive genomics and plausible inhibitors for MurA and MurB. Kaur N, Khokhar M, Jain V, Bharatam PV, Sandhir R, Tewari R. Appl. Biochem. Biotechnol. 171 417-436 (2013)
  20. Benzothioxalone derivatives as novel inhibitors of UDP-N-acetylglucosamine enolpyruvyl transferases (MurA and MurZ). Miller K, Dunsmore CJ, Leeds JA, Patching SG, Sachdeva M, Blake KL, Stubbings WJ, Simmons KJ, Henderson PJ, De Los Angeles J, Fishwick CW, Chopra I. J. Antimicrob. Chemother. 65 2566-2573 (2010)
  21. Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective. Klein CD, Bachelier A. J. Comput. Aided Mol. Des. 20 621-628 (2006)
  22. Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus. Kim MK, Cho MK, Song HE, Kim D, Park BH, Lee JH, Kang GB, Kim SH, Im YJ, Lee DS, Eom SH. Proteins 66 751-754 (2007)
  23. Differential antibacterial properties of the MurA inhibitors terreic acid and fosfomycin. Olesen SH, Ingles DJ, Yang Y, Schönbrunn E. J. Basic Microbiol. 54 322-326 (2014)
  24. Inhibitory mechanism of the Qβ lysis protein A2. Reed CA, Langlais C, Kuznetsov V, Young R. Mol. Microbiol. 86 836-844 (2012)
  25. Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis. Oberdorfer G, Binter A, Ginj C, Macheroux P, Gruber K. J. Biol. Chem. 287 31427-31436 (2012)
  26. Studies on the biodegradation of fosfomycin: growth of Rhizobium huakuii PMY1 on possible intermediates synthesised chemically. McGrath JW, Hammerschmidt F, Preusser W, Quinn JP, Schweifer A. Org. Biomol. Chem. 7 1944-1953 (2009)
  27. 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. Thomas AM, Ginj C, Jelesarov I, Amrhein N, Macheroux P. Eur. J. Biochem. 271 2682-2690 (2004)
  28. UDP-N-acetylglucosamine enolpyruvyl transferase from Pseudomonas aeruginosa Dube S, Nanda K, Rani R, Kaur NJ, Nagpal JK, Upadhyay DJ, Cliffe IA, Saini KS, Purnapatre KP. World J. Microbiol. Biotechnol. 26 1623-1629 (2010)
  29. Cloning, expression and characterization of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from Wolbachia endosymbiont of human lymphatic filarial parasite Brugia malayi. Shahab M, Verma M, Pathak M, Mitra K, Misra-Bhattacharya S. PLoS ONE 9 e99884 (2014)
  30. On the conversion of structural analogues of (S)-2-hydroxypropylphosphonic acid to epoxides by the final enzyme of fosfomycin biosynthesis in S. fradiae. Schweifer A, Hammerschmidt F. Bioorg. Med. Chem. Lett. 18 3056-3059 (2008)
  31. Evaluating low level sequence identities. Are Aspergillus QUTA and AROM homologous? Nicholas HB, Arst HN, Caddick MX. Eur. J. Biochem. 268 414-419 (2001)
  32. UDP-N-Acetylglucosamine enolpyruvyl transferase (MurA) of Acinetobacter baumannii (AbMurA): Structural and functional properties. Sonkar A, Shukla H, Shukla R, Kalita J, Pandey T, Tripathi T. Int. J. Biol. Macromol. 97 106-114 (2017)
  33. Identification of a novel fosfomycin-resistant UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from a soil metagenome. Cheng G, Hu Y, Lu N, Li J, Wang Z, Chen Q, Zhu B. Biotechnol. Lett. 35 273-278 (2013)
  34. Fosfomycin and Comparator Activity Against Select Enterobacteriaceae, Pseudomonas, and Enterococcus Urinary Tract Infection Isolates from the United States in 2012. Keepers TR, Gomez M, Celeri C, Krause KM, Biek D, Critchley I. Infect Dis Ther 6 233-243 (2017)
  35. Discovery of new MurA inhibitors using induced-fit simulation and docking. Rožman K, Lešnik S, Brus B, Hrast M, Sova M, Patin D, Barreteau H, Konc J, Janežič D, Gobec S. Bioorg. Med. Chem. Lett. 27 944-949 (2017)
  36. Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme from Pseudomonas aeruginosa. Lima AH, Dos Santos AM, Alves CN, Lameira J. Chem Biol Drug Des 89 599-607 (2017)
  37. Molecular Basis for Resistance Against Phosphonate Antibiotics and Herbicides. Chekan JR, Cogan DP, Nair SK. Medchemcomm 7 28-36 (2016)
  38. Fluorimetric analysis of the binding characteristics of 5-enolpyruvylshikimate-3-phosphate synthase with substrates in Dunaliella salina. Cao Y, Xu H, Xie L, Yi Y, Yu Y, Feng S, Qiao D, Cao Y. J. Basic Microbiol. 54 937-944 (2014)
  39. Suppressor Mutations Linking gpsB with the First Committed Step of Peptidoglycan Biosynthesis in Listeria monocytogenes. Rismondo J, Bender JK, Halbedel S. J. Bacteriol. 199 (2017)
  40. Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Schmidt R, Jager V, Zühlke D, Wolff C, Bernhardt J, Cankar K, Beekwilder J, Ijcken WV, Sleutels F, Boer W, Riedel K, Garbeva P. Sci Rep 7 862 (2017)


Related citations provided by authors (1)