› 1q8f

X-ray diffraction
1.7Å resolution

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

Released:
DOI: 10.2210/pdb1q8f/pdb
PDB entry 1q8f coloured by chain, front view.
PDB entry 1q8f coloured by chain, side view.
PDB entry 1q8f coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
Giabbai B, Degano M
Structure 12 739-49 (2004)
PMID: 15130467

Function and Biology Details

Reaction catalysed: 
A pyrimidine nucleoside + H(2)O = D-ribose + a pyrimidine base
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152532 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrimidine-specific ribonucleoside hydrolase RihB Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 313 amino acids
Theoretical weight: 33.76 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P33022 (Residues: 1-313; Coverage: 100%)
Gene names: JW2149, b2162, rihB, yeiK
Sequence domains: Inosine-uridine preferring nucleoside hydrolase
Structure domains: Ribonucleoside hydrolase-like

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand GOL 16 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P1
Unit cell:
a: 44.808Å b: 85.707Å c: 90.678Å
α: 112.95° β: 101.95° γ: 85.92°
R-values:
R R work R free
0.153 0.153 0.17
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases.
Degano M. (2022)
16 other articles

4 mentions without citation

Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses.
Shaposhnikov et al. (2023)
3 more