Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

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This is version 1.3 of the entry. See complete history


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.

(2004) Structure 12: 739-749

  • DOI: https://doi.org/10.1016/j.str.2004.03.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Enzymes with nucleoside hydrolase (NH) activity are crucial for salvaging nucleic acid components in purine auxotrophic protozoan parasites, but are also present in prokaryotes and higher eukaryotes. Here we analyze the distribution of genes encoding for putative NH proteins and characterize the yeiK gene product from Escherichia coli as a pyrimidine-specific NH. The crystal structure of YeiK to 1.7 A defines the structural basis for its substrate specificity and identifies residues involved in the catalytic mechanism that differ from both nonspecific and purine-specific NHs. Large differences in the tetrameric quaternary structure compared to nonspecific protozoan NHs are brought forth by minor differences in the interacting surfaces. The first structural and functional characterization of a nonparasitic, pyrimidine nucleoside-specific NH suggests a possible role for these enzymes in the metabolism of tRNA nucleosides. The high catalytic efficiency of YeiK toward 5-fluorouridine could be exploited for suicide gene therapy in cancer treatment.

  • Organizational Affiliation

    Biocrystallography Unit, DIBIT, San Raffaele Scientific Institute, via Olgettina 58, I-20132 Milan, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine nucleoside hydrolase
A, B, C, D
313Escherichia coliMutation(s): 0 
Gene Names: YEIK
Find proteins for P33022 (Escherichia coli (strain K12))
Explore P33022 
Go to UniProtKB:  P33022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33022
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
C3 H8 O3
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
O [auth C],
T [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.808α = 112.95
b = 85.707β = 101.95
c = 90.678γ = 85.92
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description