4C5A image
Deposition Date 2013-09-10
Release Date 2015-01-21
Last Version Date 2023-12-20
Entry Detail
PDB ID:
4C5A
Keywords:
LIGASE
Title:
The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate
Biological Source:
Source Organism:
ESCHERICHIA COLI K-12 (Taxon ID: 83333)
synthetic construct (Taxon ID: 32630)
Host Organism:
ESCHERICHIA COLI BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.65 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
4C5A validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:D-ALANINE--D-ALANINE LIGASE
Chain IDs:A, B
Chain Length:330
Number of Molecules:2
Biological Source:ESCHERICHIA COLI K-12
UniProt ID:P07862 Pfam ID:PF01820, PF07478
Polymer Type:polypeptide(L)
Molecule:PEPTIDE
Chain IDs:C
Chain Length:8
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
ADP
DS0
GOL
MG
Primary Citation
Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
Nat Commun 8 1939 1939 (2017)
PMID: 29208891 DOI: 10.1038/s41467-017-02118-7

Abstact

D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4C5B
4C5C