› 3mkn

X-ray diffraction
2Å resolution

Crystal structure of the E. coli pyrimidine nucleosidase YeiK bound to a competitive inhibitor

Released:
DOI: 10.2210/pdb3mkn/pdb
PDB entry 3mkn coloured by chain, front view.
PDB entry 3mkn coloured by chain, side view.
PDB entry 3mkn 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

2 bound ligands:
Ligand CA 4 x CA
Ligand DNB 4 x DNB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 84.851Å b: 86.446Å c: 97.817Å
α: 90° β: 98.86° γ: 90°
R-values:
R R work R free
0.175 0.174 0.196
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases.
Degano M. (2022)
1 more