› 3mkm

X-ray diffraction
2.2Å resolution

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)

Released:
DOI: 10.2210/pdb3mkm/pdb
PDB entry 3mkm coloured by chain, front view.
PDB entry 3mkm coloured by chain, side view.
PDB entry 3mkm coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Energy landscapes associated with macromolecular conformational changes from endpoint structures.
Fornili A, Giabbai B, Garau G, Degano M
J Am Chem Soc 132 17570-7 (2010)
PMID: 21082835

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 analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111211 (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: 316 amino acids
Theoretical weight: 34.04 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C3T3U2 (Residues: 1-313; Coverage: 100%)
Gene names: ECs3054, rihB
Sequence domains: Inosine-uridine preferring nucleoside hydrolase
Structure domains: Ribonucleoside hydrolase-like

Ligands and Environments

1 bound ligand:
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P1
Unit cell:
a: 45.601Å b: 85.231Å c: 90.06Å
α: 66.65° β: 79.39° γ: 85.3°
R-values:
R R work R free
0.187 0.185 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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

1 mention without citation

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