› 1f06

X-ray diffraction
2.1Å resolution

THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE

Released:
DOI: 10.2210/pdb1f06/pdb
PDB entry 1f06 coloured by chain, front view.
PDB entry 1f06 coloured by chain, side view.
PDB entry 1f06 coloured by chain, top view.
Source organism: Corynebacterium glutamicum
Primary publication:
The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
Cirilli M, Scapin G, Sutherland A, Vederas JC, Blanchard JS
Protein Sci 9 2034-7 (2000)
PMID: 11106178

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 domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-138297 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Meso-diaminopimelate D-dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 320 amino acids
Theoretical weight: 35.24 KDa
Source organism: Corynebacterium glutamicum
Expression system: Escherichia coli
UniProt:
  • Canonical: P04964 (Residues: 1-320; Coverage: 100%)
Gene names: Cgl2617, cg2900, ddh
Sequence domains: Diaminopimelic acid dehydrogenase C-terminal domain
Structure domains:

Ligands and Environments


Cofactor: Ligand NDP 2 x NDP
1 bound ligand:
Ligand 2NP 1 x 2NP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P21
Unit cell:
a: 75.547Å b: 65.591Å c: 84.281Å
α: 90° β: 106.52° γ: 90°
R-values:
R R work R free
0.197 0.179 0.209
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Artificial Thermostable D-Amino Acid Dehydrogenase: Creation and Application.
Akita et al. (2018)
11 other articles

5 mentions without citation

Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies.
Chen et al. (2018)
4 more