› 1so3

X-ray diffraction
1.9Å resolution

Crystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate

Released:
DOI: 10.2210/pdb1so3/pdb
PDB entry 1so3 coloured by chain, front view.
PDB entry 1so3 coloured by chain, side view.
PDB entry 1so3 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.
Wise EL, Yew WS, Gerlt JA, Rayment I
Biochemistry 43 6438-46 (2004)
PMID: 15157078

Function and Biology Details

Reaction catalysed: 
3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-153861 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-keto-L-gulonate-6-phosphate decarboxylase UlaD Chains: A, B
Molecule details ›
Chains: A, B
Length: 216 amino acids
Theoretical weight: 23.54 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P39304 (Residues: 1-216; Coverage: 100%)
Gene names: JW4154, b4196, sgaH, ulaD, yjfV
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand TX4 2 x TX4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 123.116Å b: 42.059Å c: 91.07Å
α: 90° β: 97.06° γ: 90°
R-values:
R R work R free
0.15 0.148 0.192
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt et al. (2015)
1 more

2 mentions without citation

Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.
Xu et al. (2018)
1 more