› 6g59

X-ray diffraction
2.45Å resolution

Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative

Released:
DOI: 10.2210/pdb6g59/pdb
PDB entry 6g59 coloured by chain, front view.
PDB entry 6g59 coloured by chain, side view.
PDB entry 6g59 coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus Mu50
Primary publication:
Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.
Hoegl A, Nodwell MB, Kirsch VC, Bach NC, Pfanzelt M, Stahl M, Schneider S, Sieber SA
Nat Chem 10 1234-1245 (2018)
PMID: 30297752

Function and Biology Details

Reaction catalysed: 
L-alanine = D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159103 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alanine racemase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 404 amino acids
Theoretical weight: 45.29 KDa
Source organism: Staphylococcus aureus subsp. aureus Mu50
Expression system: Escherichia coli
UniProt:
  • Canonical: P63479 (Residues: 2-382; Coverage: 100%)
Gene names: SAV2070, alr, alr1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand EM2 2 x EM2
Ligand SO4 6 x SO4
Ligand NA 4 x NA
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 85.924Å b: 106.855Å c: 131.023Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.215
Expression system: Escherichia coli

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Citations

12 review citations

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis.
Richts et al. (2019)
11 more

1 mention without citation

Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.
Hoegl et al. (2018)