› 2c54

X-ray diffraction
1.5Å resolution

gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.

Released:
DOI: 10.2210/pdb2c54/pdb
PDB entry 2c54 coloured by chain, front view.
PDB entry 2c54 coloured by chain, side view.
PDB entry 2c54 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.
Major LL, Wolucka BA, Naismith JH
J Am Chem Soc 127 18309-20 (2005)
PMID: 16366586

Function and Biology Details

Reaction catalysed: 
GDP-alpha-D-mannose = GDP-beta-L-gulose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188149 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose 3,5-epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 379 amino acids
Theoretical weight: 42.97 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q93VR3 (Residues: 1-377; Coverage: 100%)
Gene names: At5g28840, F7P1.20
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
4 bound ligands:
Ligand GKE 2 x GKE
Ligand GKD 2 x GKD
Ligand FMT 18 x FMT
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 62.278Å b: 82.457Å c: 65.875Å
α: 90° β: 98.77° γ: 90°
R-values:
R R work R free
0.121 0.118 0.167
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

The structure, function, and biosynthesis of plant cell wall pectic polysaccharides.
Caffall et al. (2009)
8 more

14 mentions without citation

GDP-Mannose 3,5-Epimerase: A View on Structure, Mechanism, and Industrial Potential.
Beerens et al. (2021)
13 more