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The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).

Roper DI, Huyton T, Vagin A, Dodson G
Proc Natl Acad Sci U S A 97 8921-5 (2000)
Cited: 37 times
EuropePMC logo PMID: 10908650

Abstract

d-alanine-d-lactate ligase from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been determined with data extending to 2.5-A resolution. This structure shows that the active site has unexpected interactions and is distinct from previous models for d-alanyl-d-lactate ligase mechanistic studies. It appears that the preference of the enzyme for lactate as a ligand over d-alanine could be mediated by electrostatic effects and/or a hydrogen-bonding network, which principally involve His-244. The structure of d-alanyl-d-lactate ligase provides a revised interpretation of the molecular events that lead to vancomycin resistance.

Reviews - 1e4e mentioned but not cited (2)

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  2. Molecular mechanisms of vancomycin resistance. Stogios PJ, Savchenko A. Protein Sci 29 654-669 (2020)

Articles - 1e4e mentioned but not cited (8)

  1. The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Roper DI, Huyton T, Vagin A, Dodson G. Proc Natl Acad Sci U S A 97 8921-8925 (2000)
  2. Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis. Shomura Y, Hinokuchi E, Ikeda H, Senoo A, Takahashi Y, Saito J, Komori H, Shibata N, Yonetani Y, Higuchi Y. Protein Sci 21 707-716 (2012)
  3. Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis. Meziane-Cherif D, Saul FA, Haouz A, Courvalin P. J Biol Chem 287 37583-37592 (2012)
  4. OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries. Wu Y, Dousis AD, Chen M, Li J, Ma J. J Mol Biol 385 1314-1329 (2009)
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  8. Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Rahman MA, Kaiser F, Jamshidi S, Freitas Monteiro M, Rahman KM, Mullany P, Roberts AP. Sci Rep 10 20709 (2020)


Reviews citing this publication (7)

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  1. Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies. Liu S, Chang JS, Herberg JT, Horng MM, Tomich PK, Lin AH, Marotti KR. Proc Natl Acad Sci U S A 103 15178-15183 (2006)
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  3. In vitro activity of alpha-mangostin in killing and eradicating Staphylococcus epidermidis RP62A biofilms. Sivaranjani M, Prakash M, Gowrishankar S, Rathna J, Pandian SK, Ravi AV. Appl Microbiol Biotechnol 101 3349-3359 (2017)
  4. Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Batson S, de Chiara C, Majce V, Lloyd AJ, Gobec S, Rea D, Fülöp V, Thoroughgood CW, Simmons KJ, Dowson CG, Fishwick CWG, de Carvalho LPS, Roper DI. Nat Commun 8 1939 (2017)
  5. Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB). Sova M, Cadez G, Turk S, Majce V, Polanc S, Batson S, Lloyd AJ, Roper DI, Fishwick CW, Gobec S. Bioorg Med Chem Lett 19 1376-1379 (2009)
  6. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke S, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M, Schlüter A. Biotechnol Biofuels 6 49 (2013)
  7. Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach. Sivaranjani M, Leskinen K, Aravindraja C, Saavalainen P, Pandian SK, Skurnik M, Ravi AV. Front Microbiol 10 150 (2019)
  8. Efficacy of novel antibacterial compounds targeting histidine kinase YycG protein. Liu H, Zhao D, Chang J, Yan L, Zhao F, Wu Y, Xu T, Gong T, Chen L, He N, Wu Y, Han S, Qu D. Appl Microbiol Biotechnol 98 6003-6013 (2014)
  9. A de novo designed inhibitor of D-Ala-D-Ala ligase from E. coli. Besong GE, Bostock JM, Stubbings W, Chopra I, Roper DI, Lloyd AJ, Fishwick CW, Johnson AP. Angew Chem Int Ed Engl 44 6403-6406 (2005)
  10. Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori. Wu D, Zhang L, Kong Y, Du J, Chen S, Chen J, Ding J, Jiang H, Shen X. Proteins 72 1148-1160 (2008)
  11. Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes. Lee JH, Na Y, Song HE, Kim D, Park BH, Rho SH, Im YJ, Kim MK, Kang GB, Lee DS, Eom SH. Proteins 64 1078-1082 (2006)
  12. Structural features of the Cu(2+)-vancomycin complex. Kucharczyk M, Brzezowska M, Maciag A, Lis T, Jezowska-Bojczuk M. J Inorg Biochem 102 936-942 (2008)
  13. Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features. Panvert M, Dubiez E, Arnold L, Perez J, Mechulam Y, Seufert W, Schmitt E. Structure 23 1596-1608 (2015)
  14. Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan. Hashimoto Y, Kurushima J, Nomura T, Tanimoto K, Tamai K, Yanagisawa H, Shirabe K, Ike Y, Tomita H. BMC Microbiol 18 213 (2018)
  15. Population structure, epidemiology and antibiotic resistance patterns of Streptococcus pneumoniae serotype 5: prior to PCV-13 vaccine introduction in Eastern Gambia. Ashu EE, Jarju S, Dione M, Mackenzie G, Ikumapayi UN, Manjang A, Azuine R, Antonio M. BMC Infect Dis 16 33 (2016)
  16. Crystallization and preliminary X-ray analysis of a D-alanyl-D-alanine ligase (EcDdlB) from Escherichia coli. Batson S, Rea D, Fülöp V, Roper DI. Acta Crystallogr Sect F Struct Biol Cryst Commun 66 405-408 (2010)
  17. D-Ala:D-Ala ligase gene flanking the vanC cluster: evidence for presence of three ligase genes in vancomycin-resistant Enterococcus gallinarum BM4174. Ambúr OH, Reynolds PE, Arias CA. Antimicrob Agents Chemother 46 95-100 (2002)
  18. Substrate Inhibition of VanA by d-Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner. van der Aart LT, Lemmens N, van Wamel WJ, van Wezel GP. Antimicrob Agents Chemother 60 4930-4939 (2016)
  19. Insight into Kytococcus schroeteri Infection Management: A Case Report and Review. Bagelman S, Zvigule-Neidere G. Infect Dis Rep 13 230-238 (2021)
  20. Genomic analysis of Enterococcus faecium strain RAOG174 associated with acute chorioamnionitis carried antibiotic resistance gene: is it time for precise microbiological identification for appropriate antibiotic use? Pongchaikul P, Romero R, Mongkolsuk P, Vivithanaporn P, Wongsurawat T, Jenjaroenpun P, Nitayanon P, Thaipisuttikul I, Kamlungkuea T, Singsaneh A, Santanirand P, Chaemsaithong P. BMC Genomics 24 405 (2023)


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