› 1npd

X-ray diffraction
2.3Å resolution

X-RAY STRUCTURE OF SHIKIMATE DEHYDROGENASE COMPLEXED WITH NAD+ FROM E.COLI (YDIB) NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER24

Released:
DOI: 10.2210/pdb1npd/pdb
PDB entry 1npd coloured by chain, front view.
PDB entry 1npd coloured by chain, side view.
PDB entry 1npd coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.
Benach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF
J Biol Chem 278 19176-82 (2003)
PMID: 12624088

Function and Biology Details

Reaction catalysed: 
L-quinate + NAD(P)(+) = 3-dehydroquinate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141300 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Quinate/shikimate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 288 amino acids
Theoretical weight: 31.77 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A6D5 (Residues: 1-288; Coverage: 100%)
Gene name: ydiB
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
No bound ligands
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P64
Unit cell:
a: 157.185Å b: 157.185Å c: 39.782Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.217 0.274
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework.
Peek et al. (2015)
22 other articles

2 mentions without citation

Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
Singh et al. (2005)
1 more