› 3mj4

X-ray diffraction
2.65Å resolution

Crystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose

Released:
DOI: 10.2210/pdb3mj4/pdb
PDB entry 3mj4 coloured by chain, front view.
PDB entry 3mj4 coloured by chain, side view.
PDB entry 3mj4 coloured by chain, top view.
Source organism: Deinococcus radiodurans R1
Primary publication:
Chemoenzymatic synthesis, inhibition studies, and X-ray crystallographic analysis of the phosphono analog of UDP-Galp as an inhibitor and mechanistic probe for UDP-galactopyranose mutase.
Partha SK, Sadeghi-Khomami A, Slowski K, Kotake T, Thomas NR, Jakeman DL, Sanders DA
J Mol Biol 403 578-90 (2010)
PMID: 20850454

Function and Biology Details

Reaction catalysed: 
UDP-alpha-D-galactopyranose = UDP-alpha-D-galactofuranose
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193354 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-galactopyranose mutase C-terminal domain-containing protein Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 397 amino acids
Theoretical weight: 45.74 KDa
Source organism: Deinococcus radiodurans R1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RYF1 (Residues: 1-397; Coverage: 100%)
Gene name: DR_A0367
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand FAD 10 x FAD
4 bound ligands:
Ligand UDP 9 x UDP
Ligand GOL 25 x GOL
Ligand URM 1 x URM
Ligand XYL 2 x XYL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 134.149Å b: 175.715Å c: 223.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.207 0.262
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

2 mentions without citation

Structure, mechanism, and dynamics of UDP-galactopyranose mutase.
Tanner et al. (2014)
1 more