1Q8F

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history. 


Literature

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:  
    1Q8F

  • 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 ...

    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.

    Related Citations: 
    • Three-dimensional structure of the Inosine-Uridine Nucleoside N-ribohydrolase from Crithidia fasciculata
      Degano, M., Gopaul, D.N., Scapin, G., Schramm, V.L., Sacchettini, J.C.
      (1996) Biochemistry 35: 5971
    • Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
      Degano, M., Almo, S.C., Sacchettini, J.C., Schramm, V.L.
      (1998) Biochemistry 37: 6277
    • Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax
      Versees, W., Decanniere, K., Pelle, R., Depoorter, J., Brosens, E., Parkin, D.W., Steyaert, J.
      (2001) J Mol Biol 307: 1363
    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrimidine nucleoside hydrolaseA, B, C, D313Escherichia coliMutation(s): 0 
Gene Names: yeiK
EC: 3.2.2.8
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
O [auth C],
T [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

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