› 2gmu

X-ray diffraction
1.9Å resolution

Crystal structure of E coli GDP-4-keto-6-deoxy-D-mannose-3-dehydratase complexed with PLP-glutamate ketimine intermediate

Released:
DOI: 10.2210/pdb2gmu/pdb
PDB entry 2gmu coloured by chain, front view.
PDB entry 2gmu coloured by chain, side view.
PDB entry 2gmu coloured by chain, top view.
Source organism: Escherichia coli O55:H7
Primary publication:
The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme.
Cook PD, Thoden JB, Holden HM
Protein Sci 15 2093-106 (2006)
PMID: 16943443

Function and Biology Details

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-190234 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
WbdK Chains: A, B
Molecule details ›
Chains: A, B
Length: 390 amino acids
Theoretical weight: 44.35 KDa
Source organism: Escherichia coli O55:H7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9F118 (Residues: 1-388; Coverage: 100%)
Gene names: NCTC8959_01918, wbdK
Sequence domains: DegT/DnrJ/EryC1/StrS aminotransferase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand PDG 2 x PDG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 74.9Å b: 88Å c: 126Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.231
Expression system: Escherichia coli

Quick links

Citations

4 review citations

The structural biology of enzymes involved in natural product glycosylation.
Singh et al. (2012)
3 more

3 mentions without citation

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Dana et al. (2019)
2 more