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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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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: https://doi.org/10.1186/1472-6807-10-14
  • Primary Citation of Related Structures:  

  • 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. Here, we report the first crystal structure of a CU-NH bound to a competitive inhibitor, the complex between the Escherichia coli enzyme RihA bound to 3, 4-diaminophenyl-iminoribitol (DAPIR) to a resolution of 2.1 A. The ligand can bind at the active site in two distinct orientations, and the stabilization of two flexible active site regions is pivotal to establish the interactions required for substrate discrimination and catalysis. A comparison with the product-bound RihA structure allows a rationalization of the structural rearrangements required for an enzymatic catalytic cycle, highlighting a substrate-assisted cooperative motion, and suggesting a yet overlooked role of the conserved His82 residue in modulating product release. Differences in the structural features of the active sites in the two homologous CU-NHs RihA and RihB from E. coli provide a rationale for their fine differences in substrate specificity. These new findings hint at a possible role of CU-NHs in the breakdown of modified nucleosides derived from RNA molecules.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine-specific ribonucleoside hydrolase rihA
A, B, C, D
312Escherichia coli K-12Mutation(s): 0 
Gene Names: ybeK
Find proteins for P41409 (Escherichia coli (strain K12))
Explore P41409 
Go to UniProtKB:  P41409
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41409
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DNB

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]
C11 H17 N3 O3
Query on BME

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C2 H6 O S
Query on CA

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F [auth A],
H [auth B],
J [auth C],
L [auth D]
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
XSCALEdata scaling

Structure Validation

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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
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description