› 4daa

X-ray diffraction
2.4Å resolution

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE IN PYRIDOXAL-5'-PHOSPHATE (PLP) FORM

Released:
DOI: 10.2210/pdb4daa/pdb
PDB entry 4daa coloured by chain, front view.
PDB entry 4daa coloured by chain, side view.
PDB entry 4daa coloured by chain, top view.
Source organism: Bacillus sp. YM-1
Primary publication:
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D
Biochemistry 37 4958-67 (1998)
PMID: 9538014

Function and Biology Details

Reaction catalysed: 
D-alanine + 2-oxoglutarate = pyruvate + D-glutamate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148806 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine aminotransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 277 amino acids
Theoretical weight: 31.72 KDa
Source organism: Bacillus sp. YM-1
Expression system: Escherichia coli
UniProt:
  • Canonical: P19938 (Residues: 2-278; Coverage: 98%)
Gene name: dat
Sequence domains: Amino-transferase class IV
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: C2
Unit cell:
a: 141.1Å b: 68.9Å c: 87.4Å
α: 90° β: 119.5° γ: 90°
R-values:
R R work R free
0.181 0.181 0.247
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations.
Eliot et al. (2004)
9 more

1 mention without citation

Structural Snapshots of an Engineered Cystathionine-γ-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site.
Yan et al. (2017)