› 5n9m

X-ray diffraction
1.85Å resolution

Crystal structure of GatD - a glutamine amidotransferase from Staphylococcus aureus involved in peptidoglycan amidation

Released:
DOI: 10.2210/pdb5n9m/pdb
PDB entry 5n9m coloured by chain, front view.
PDB entry 5n9m coloured by chain, side view.
PDB entry 5n9m coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus COL
Primary publication:
First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD.
Leisico F, V Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trinc��o J, Rom��o MJ, de Lencastre H, Santos-Silva T
Sci Rep 8 5313 (2018)
PMID: 29593310

Function and Biology Details

Reactions catalysed: 
L-glutamine + H(2)O = L-glutamate + NH(3)
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101624 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD Chains: A, B
Molecule details ›
Chains: A, B
Length: 243 amino acids
Theoretical weight: 27.47 KDa
Source organism: Staphylococcus aureus subsp. aureus COL
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H2WZ38 (Residues: 1-243; Coverage: 100%)
Gene names: SACOL1950, gatD
Sequence domains: CobB/CobQ-like glutamine amidotransferase domain

Ligands and Environments

2 bound ligands:
Ligand GLN 1 x GLN
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 48.61Å b: 93.92Å c: 110.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.149 0.186
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Assessment and Comparison of Database Search Engines for Peptidomic Applications.
De La Toba et al. (2023)
5 more

3 mentions without citation

First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD.
Leisico et al. (2018)
2 more