› 1rpn

X-ray diffraction
2.15Å resolution

Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH

Released:
DOI: 10.2210/pdb1rpn/pdb
PDB entry 1rpn coloured by chain, front view.
PDB entry 1rpn coloured by chain, side view.
PDB entry 1rpn coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Webb NA, Mulichak AM, Lam JS, Rocchetta HL, Garavito RM
Protein Sci 13 529-39 (2004)
PMID: 14739333

Function and Biology Details

Reaction catalysed: 
GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-175920 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose 4,6-dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 335 amino acids
Theoretical weight: 37.85 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q51366 (Residues: 1-323; Coverage: 100%)
Gene names: PA5453, gca, gmd
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NDP 4 x NDP
1 bound ligand:
Ligand GDP 4 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P3221
Unit cell:
a: 125.73Å b: 125.73Å c: 220.025Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.176 0.174 0.196
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Natural-product sugar biosynthesis and enzymatic glycodiversification.
Thibodeaux et al. (2008)
3 more

5 mentions without citation

Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Webb et al. (2004)
4 more