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Structure paper

TitleStructure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition.
Journal, issue, pagesStructure, Vol. 22, Page 949-960, Year 2014
Publish dateMar 5, 2013 (structure data deposition date)
AuthorsHoyland, C.N. / Aldridge, C. / Cleverley, R.M. / Duchene, M.C. / Minasov, G. / Onopriyenko, O. / Sidiq, K. / Stogios, P.J. / Anderson, W.F. / Daniel, R.A. ...Hoyland, C.N. / Aldridge, C. / Cleverley, R.M. / Duchene, M.C. / Minasov, G. / Onopriyenko, O. / Sidiq, K. / Stogios, P.J. / Anderson, W.F. / Daniel, R.A. / Savchenko, A. / Vollmer, W. / Lewis, R.J.
External linksStructure / PubMed:24909784
MethodsX-ray diffraction
Resolution1.8 - 2.8 Å
Structure data

PDB-4jid:
Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-free
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4mph:
Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-bound
Method: X-RAY DIFFRACTION / Resolution: 2.0301 Å

PDB-4ox3:
Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-4ox5:
Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4oxd:
Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

Chemicals

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

ChemComp-PE3:
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL

ChemComp-PO4:
PHOSPHATE ION

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

ChemComp-DAL:
D-ALANINE

ChemComp-MG:
Unknown entry

ChemComp-LYS:
LYSINE

ChemComp-MUB:
N-acetyl-alpha-muramic acid

Source
  • bacillus anthracis (anthrax bacterium)
  • bacillus subtilis (bacteria)
  • streptococcus pneumoniae (bacteria)
  • streptococcus pneumoniae r6 (bacteria)
  • lactobacillus acidophilus (bacteria)
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / D-alanyl-D-alanine carboxypeptidase / BaLdcB / L / D-carboxypeptidase / tetrapeptidase / substrate L-Ala-D-iso-Gln-L-Lys-D-Ala / Hedgehog/DD-peptidase fold / VanY-like family / MEROPS family M15B / zinc-dependent metallopeptidase / peptidoglycan metallopeptidase / LAS family / LD-carboxypeptidase / Cell wall modifying enzyme

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