Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1997 Jun 15;16(12):3416–3425. doi: 10.1093/emboj/16.12.3416

Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.

J A Bertrand 1, G Auger 1, E Fanchon 1, L Martin 1, D Blanot 1, J van Heijenoort 1, O Dideberg 1
PMCID: PMC1169967  PMID: 9218784

Abstract

UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal structure of MurD in the presence of its substrate UMA has been solved to 1.9 A resolution. Phase information was obtained from multiple anomalous dispersion using the K-shell edge of selenium in combination with multiple isomorphous replacement. The structure comprises three domains of topology each reminiscent of nucleotide-binding folds: the N- and C-terminal domains are consistent with the dinucleotide-binding fold called the Rossmann fold, and the central domain with the mononucleotide-binding fold also observed in the GTPase family. The structure reveals the binding site of the substrate UMA, and comparison with known NTP complexes allows the identification of residues interacting with ATP. The study describes the first structure of the UDP-N-acetylmuramoyl-peptide ligase family.

Full Text

The Full Text of this article is available as a PDF (781.5 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Benson T. E., Filman D. J., Walsh C. T., Hogle J. M. An enzyme-substrate complex involved in bacterial cell wall biosynthesis. Nat Struct Biol. 1995 Aug;2(8):644–653. doi: 10.1038/nsb0895-644. [DOI] [PubMed] [Google Scholar]
  2. Berchtold H., Reshetnikova L., Reiser C. O., Schirmer N. K., Sprinzl M., Hilgenfeld R. Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature. 1993 Sep 9;365(6442):126–132. doi: 10.1038/365126a0. [DOI] [PubMed] [Google Scholar]
  3. Dale R. M., Livingston D. C., Ward D. C. The synthesis and enzymatic polymerization of nucleotides containing mercury: potential tools for nucleic acid sequencing and structural analysis. Proc Natl Acad Sci U S A. 1973 Aug;70(8):2238–2242. doi: 10.1073/pnas.70.8.2238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dale R. M., Martin E., Livingston D. C., Ward D. C. Direct covalent mercuration of nucleotides and polynucleotides. Biochemistry. 1975 Jun 3;14(11):2447–2457. doi: 10.1021/bi00682a027. [DOI] [PubMed] [Google Scholar]
  5. Diederichs K., Schulz G. E. Three-dimensional structure of the complex between the mitochondrial matrix adenylate kinase and its substrate AMP. Biochemistry. 1990 Sep 4;29(35):8138–8144. doi: 10.1021/bi00487a022. [DOI] [PubMed] [Google Scholar]
  6. Dreusicke D., Schulz G. E. The glycine-rich loop of adenylate kinase forms a giant anion hole. FEBS Lett. 1986 Nov 24;208(2):301–304. doi: 10.1016/0014-5793(86)81037-7. [DOI] [PubMed] [Google Scholar]
  7. Fan C., Moews P. C., Shi Y., Walsh C. T., Knox J. R. A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Feb 14;92(4):1172–1176. doi: 10.1073/pnas.92.4.1172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fan C., Moews P. C., Walsh C. T., Knox J. R. Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution. Science. 1994 Oct 21;266(5184):439–443. doi: 10.1126/science.7939684. [DOI] [PubMed] [Google Scholar]
  9. Gaboriaud C., Bissery V., Benchetrit T., Mornon J. P. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 1987 Nov 16;224(1):149–155. doi: 10.1016/0014-5793(87)80439-8. [DOI] [PubMed] [Google Scholar]
  10. Hendrickson W. A., Smith J. L., Phizackerley R. P., Merritt E. A. Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins. 1988;4(2):77–88. doi: 10.1002/prot.340040202. [DOI] [PubMed] [Google Scholar]
  11. Henriques A. O., de Lencastre H., Piggot P. J. A Bacillus subtilis morphogene cluster that includes spoVE is homologous to the mra region of Escherichia coli. Biochimie. 1992 Jul-Aug;74(7-8):735–748. doi: 10.1016/0300-9084(92)90146-6. [DOI] [PubMed] [Google Scholar]
  12. Huang W., Jia J., Gibson K. J., Taylor W. S., Rendina A. R., Schneider G., Lindqvist Y. Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate. Biochemistry. 1995 Sep 5;34(35):10985–10995. doi: 10.1021/bi00035a004. [DOI] [PubMed] [Google Scholar]
  13. Huang W., Lindqvist Y., Schneider G., Gibson K. J., Flint D., Lorimer G. Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution. Structure. 1994 May 15;2(5):407–414. doi: 10.1016/s0969-2126(00)00042-3. [DOI] [PubMed] [Google Scholar]
  14. Ikeda M., Wachi M., Ishino F., Matsuhashi M. Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. Nucleic Acids Res. 1990 Feb 25;18(4):1058–1058. doi: 10.1093/nar/18.4.1058. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. doi: 10.1107/s0108767390010224. [DOI] [PubMed] [Google Scholar]
  16. Klein C., Chen P., Arevalo J. H., Stura E. A., Marolewski A., Warren M. S., Benkovic S. J., Wilson I. A. Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution. J Mol Biol. 1995 May 26;249(1):153–175. doi: 10.1006/jmbi.1995.0286. [DOI] [PubMed] [Google Scholar]
  17. MICHELSON A. M., DONDON J., GRUNBERG-MANAGO M. The action of polynucleotide phosphorylase on 5-halogenouridine-5' pyrophosphates. Biochim Biophys Acta. 1962 Apr 2;55:529–540. doi: 10.1016/0006-3002(62)90986-1. [DOI] [PubMed] [Google Scholar]
  18. Mengin-Lecreulx D., van Heijenoort J. Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D-Glu synthetase of Escherichia coli. Nucleic Acids Res. 1990 Jan 11;18(1):183–183. doi: 10.1093/nar/18.1.183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Michaud C., Parquet C., Flouret B., Blanot D., van Heijenoort J. Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetylmuramyl-tripeptide synthetase of Escherichia coli. Biochem J. 1990 Jul 1;269(1):277–278. doi: 10.1042/bj2690277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Noel J. P., Hamm H. E., Sigler P. B. The 2.2 A crystal structure of transducin-alpha complexed with GTP gamma S. Nature. 1993 Dec 16;366(6456):654–663. doi: 10.1038/366654a0. [DOI] [PubMed] [Google Scholar]
  21. Pai E. F., Kabsch W., Krengel U., Holmes K. C., John J., Wittinghofer A. Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature. 1989 Sep 21;341(6239):209–214. doi: 10.1038/341209a0. [DOI] [PubMed] [Google Scholar]
  22. Pai E. F., Krengel U., Petsko G. A., Goody R. S., Kabsch W., Wittinghofer A. Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 1990 Aug;9(8):2351–2359. doi: 10.1002/j.1460-2075.1990.tb07409.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Parquet C., Flouret B., Mengin-Lecreulx D., van Heijenoort J. Nucleotide sequence of the murF gene encoding the UDP-MurNAc-pentapeptide synthetase of Escherichia coli. Nucleic Acids Res. 1989 Jul 11;17(13):5379–5379. doi: 10.1093/nar/17.13.5379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Poland B. W., Silva M. M., Serra M. A., Cho Y., Kim K. H., Harris E. M., Honzatko R. B. Crystal structure of adenylosuccinate synthetase from Escherichia coli. Evidence for convergent evolution of GTP-binding domains. J Biol Chem. 1993 Dec 5;268(34):25334–25342. [PubMed] [Google Scholar]
  25. Pratviel-Sosa F., Mengin-Lecreulx D., van Heijenoort J. Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Eur J Biochem. 1991 Dec 18;202(3):1169–1176. doi: 10.1111/j.1432-1033.1991.tb16486.x. [DOI] [PubMed] [Google Scholar]
  26. RAMACHANDRAN G. N., RAMAKRISHNAN C., SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95–99. doi: 10.1016/s0022-2836(63)80023-6. [DOI] [PubMed] [Google Scholar]
  27. Ramakrishnan V., Finch J. T., Graziano V., Lee P. L., Sweet R. M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 1993 Mar 18;362(6417):219–223. doi: 10.1038/362219a0. [DOI] [PubMed] [Google Scholar]
  28. Saraste M., Sibbald P. R., Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci. 1990 Nov;15(11):430–434. doi: 10.1016/0968-0004(90)90281-f. [DOI] [PubMed] [Google Scholar]
  29. Schleifer K. H., Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972 Dec;36(4):407–477. doi: 10.1128/br.36.4.407-477.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Schönbrunn E., Sack S., Eschenburg S., Perrakis A., Krekel F., Amrhein N., Mandelkow E. Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin. Structure. 1996 Sep 15;4(9):1065–1075. doi: 10.1016/s0969-2126(96)00113-x. [DOI] [PubMed] [Google Scholar]
  31. Skarzynski T., Mistry A., Wonacott A., Hutchinson S. E., Kelly V. A., Duncan K. 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. Structure. 1996 Dec 15;4(12):1465–1474. doi: 10.1016/s0969-2126(96)00153-0. [DOI] [PubMed] [Google Scholar]
  32. Tanner Martin E., Vaganay Sabine, van Heijenoort Jean, Blanot Didier. Phosphinate Inhibitors of the D-Glutamic Acid-Adding Enzyme of Peptidoglycan Biosynthesis. J Org Chem. 1996 Mar 8;61(5):1756–1760. doi: 10.1021/jo951780a. [DOI] [PubMed] [Google Scholar]
  33. Vaganay S., Tanner M. E., van Heijenoort J., Blanot D. Study of the reaction mechanism of the D-glutamic acid-adding enzyme from Escherichia coli. Microb Drug Resist. 1996 Spring;2(1):51–54. doi: 10.1089/mdr.1996.2.51. [DOI] [PubMed] [Google Scholar]
  34. Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Yamaguchi H., Kato H., Hata Y., Nishioka T., Kimura A., Oda J., Katsube Y. Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 A resolution. J Mol Biol. 1993 Feb 20;229(4):1083–1100. doi: 10.1006/jmbi.1993.1106. [DOI] [PubMed] [Google Scholar]
  36. Yamashita M. M., Almassy R. J., Janson C. A., Cascio D., Eisenberg D. Refined atomic model of glutamine synthetase at 3.5 A resolution. J Biol Chem. 1989 Oct 25;264(30):17681–17690. doi: 10.2210/pdb2gls/pdb. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES