› 5gz1

X-ray diffraction
1.78Å resolution

Structure of substrate/cofactor-free D-amino acid dehydrogenase

Released:
DOI: 10.2210/pdb5gz1/pdb
PDB entry 5gz1 coloured by chain, front view.
PDB entry 5gz1 coloured by chain, side view.
PDB entry 5gz1 coloured by chain, top view.
Source organism: Ureibacillus thermosphaericus
Primary publication:
Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase.
Hayashi J, Seto T, Akita H, Watanabe M, Hoshino T, Yoneda K, Ohshima T, Sakuraba H
Appl Environ Microbiol 83 (2017)
PMID: 28363957

Function and Biology Details

Reaction catalysed: 
Meso-2,6-diaminoheptanedioate + H(2)O + NADP(+) = L-2-amino-6-oxoheptanedioate + NH(3) + NADPH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124238 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Meso-diaminopimelate D-dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 326 amino acids
Theoretical weight: 35.94 KDa
Source organism: Ureibacillus thermosphaericus
Expression system: Escherichia coli
UniProt:
  • Canonical: G1UII1 (Residues: 1-326; Coverage: 100%)
Gene name: ddh
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 57.364Å b: 83.201Å c: 142.241Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.231
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Enzymatic asymmetric synthesis of chiral amino acids.
Xue et al. (2018)
2 more

1 mention without citation

Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase.
Hayashi et al. (2017)