› 2fli

X-ray diffraction
1.8Å resolution

The crystal structure of D-ribulose 5-phosphate 3-epimerase from Streptococus pyogenes complexed with D-xylitol 5-phosphate

Released:
DOI: 10.2210/pdb2fli/pdb
PDB entry 2fli coloured by chain, front view.
PDB entry 2fli coloured by chain, side view.
PDB entry 2fli coloured by chain, top view.
Source organism: Streptococcus pyogenes
Primary publication:
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily.
Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA
Biochemistry 45 2493-503 (2006)
PMID: 16489742

Function and Biology Details

Reaction catalysed: 
D-ribulose 5-phosphate = D-xylulose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189455 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribulose-phosphate 3-epimerase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 220 amino acids
Theoretical weight: 23.77 KDa
Source organism: Streptococcus pyogenes
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9A1H8 (Residues: 1-220; Coverage: 100%)
Gene names: SPy_0264, rpe
Sequence domains: Ribulose-phosphate 3 epimerase family
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand ZN 12 x ZN
Ligand DX5 12 x DX5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P21
Unit cell:
a: 80.022Å b: 199.449Å c: 87.622Å
α: 90° β: 109.76° γ: 90°
R-values:
R R work R free
0.227 0.224 0.256
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study.
Cotruvo et al. (2012)
3 more

2 mentions without citation

CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii.
Lykins et al. (2018)
1 more