3G5I

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.

Garau, G.Muzzolini, L.Tornaghi, P.Degano, M.

(2010) BMC Struct Biol 10: 14-14

  • DOI: 10.1186/1472-6807-10-14
  • Primary Citation of Related Structures:  
    3G5I

  • PubMed Abstract: 
  • Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected organisms, their physiological relevance in prokaryotes and eukaryotes is yet under investigation ...

    Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected organisms, their physiological relevance in prokaryotes and eukaryotes is yet under investigation.


    Related Citations: 
    • New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product
      Muzzolini, L., Versees, W., Tornaghi, P., Van Holsbeke, E., Steyaert, J., Degano, M.
      (2006) Biochemistry 45: 773
    • 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

    Organizational Affiliation

    Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases - Scientific Institute S. Raffaele, via Olgettina 58, 20132 Milan - Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrimidine-specific ribonucleoside hydrolase rihAA, B, C, D312Escherichia coli K-12Mutation(s): 0 
Gene Names: ybeKrihAb0651JW0646
EC: 3.2.2.8 (PDB Primary Data), 3.2 (UniProt)
Find proteins for P41409 (Escherichia coli (strain K12))
Explore P41409 
Go to UniProtKB:  P41409
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.35α = 90
b = 82.91β = 112.15
c = 93.87γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-02-17
    Changes: Database references, Derived calculations