› 8hp0

X-ray diffraction
2.47Å resolution

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis

Released:
DOI: 10.2210/pdb8hp0/pdb
PDB entry 8hp0 coloured by chain, front view.
PDB entry 8hp0 coloured by chain, side view.
PDB entry 8hp0 coloured by chain, top view.
Source organism: Hoylesella timonensis
Primary publication:
Rational Design of Meso-Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d-p-Hydroxyphenylglycine.
Tan Y, Gao C, Song W, Wei W, Liu J, Gao C, Guo L, Chen X, Liu L, Wu J
Appl Environ Microbiol 89 e0010923 (2023)
PMID: 37070978

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236421 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Meso-diaminopimelate D-dehydrogenase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 299 amino acids
Theoretical weight: 32.58 KDa
Source organism: Hoylesella timonensis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A2K0XCZ3 (Residues: 1-299; Coverage: 100%)
Gene name: BFS16_11360
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand EPE 3 x EPE
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER D8 QUEST
Spacegroup: C2221
Unit cell:
a: 101.75Å b: 190.47Å c: 101.15Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.266
Expression system: Escherichia coli

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