› 4d9k

X-ray diffraction
2.19Å resolution

Crystal structure of Escherichia coli Diaminopropionate ammonia lyase in apo form

Released:
DOI: 10.2210/pdb4d9k/pdb
PDB entry 4d9k coloured by chain, front view.
PDB entry 4d9k coloured by chain, side view.
PDB entry 4d9k coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis.
Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR
J Biol Chem 287 20369-81 (2012)
PMID: 22505717

Function and Biology Details

Reaction catalysed: 
2,3-diaminopropanoate + H(2)O = pyruvate + 2 NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159191 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diaminopropionate ammonia-lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 398 amino acids
Theoretical weight: 43.45 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P66899 (Residues: 1-398; Coverage: 100%)
Gene names: JW2839, b2871, ygeX
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand PO4 4 x PO4
Ligand SO4 3 x SO4
1 modified residue:
Ligand CME 4 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21
Unit cell:
a: 85.778Å b: 94.145Å c: 94.687Å
α: 90° β: 110.01° γ: 90°
R-values:
R R work R free
0.216 0.213 0.261
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

RidA proteins prevent metabolic damage inflicted by PLP-dependent dehydratases in all domains of life.
Lambrecht et al. (2013)
6 more

1 mention without citation

Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis.
Bisht et al. (2012)