› 7dl3

X-ray diffraction
1.85Å resolution

The structure of 3,5-DAHDHcca complex with NADPH

Released:
DOI: 10.2210/pdb7dl3/pdb
PDB entry 7dl3 coloured by chain, front view.
PDB entry 7dl3 coloured by chain, side view.
PDB entry 7dl3 coloured by chain, top view.
Source organism: Candidatus Cloacimonas acidaminovorans str. Evry
Primary publication:
Crystal Structures and Catalytic Mechanism of l-erythro-3,5-Diaminohexanoate Dehydrogenase and Rational Engineering for Asymmetric Synthesis of β-Amino Acids.
Liu N, Wu L, Feng J, Sheng X, Li J, Chen X, Li J, Liu W, Zhou J, Wu Q, Zhu D
Angew Chem Int Ed Engl 60 10203-10210 (2021)
PMID: 33624917

Function and Biology Details

Reaction catalysed: 
L-erythro-3,5-diaminohexanoate + H(2)O + NAD(+) = (S)-5-amino-3-oxohexanoate + NH(3) + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109246 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alcohol dehydrogenase-like C-terminal domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 358 amino acids
Theoretical weight: 39.16 KDa
Source organism: Candidatus Cloacimonas acidaminovorans str. Evry
Expression system: Escherichia coli DH1
UniProt:
  • Canonical: B0VJ11 (Residues: 1-352; Coverage: 100%)
Gene names: CLOAM1348, kdd
Sequence domains: Zinc-binding dehydrogenase

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
1 bound ligand:
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 109.594Å b: 122.037Å c: 114.645Å
α: 90° β: 94.847° γ: 90°
R-values:
R R work R free
0.202 0.201 0.229
Expression system: Escherichia coli DH1

Quick links

Citations

1 review citation

Rational design of enzyme activity and enantioselectivity.
Song et al. (2023)

1 mention without citation

Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein coupling.
Maria-Solano et al. (2023)