Structural analysis of thermostable S. solfataricus pyrimidine-specific nucleoside hydrolase

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases from the Structures of Two Isozymes from Sulfolobus solfataricus.

Minici, C.Cacciapuoti, G.De Leo, E.Porcelli, M.Degano, M.

(2012) Biochemistry 51: 4590-4599

  • DOI: https://doi.org/10.1021/bi300209g
  • Primary Citation of Related Structures:  
    3T8I, 3T8J

  • PubMed Abstract: 

    The purine- and pyrimidine-specific nucleoside hydrolases (NHs) from the archaeon Sulfolobus solfataricus participate in the fundamental pathway of nucleotide catabolism and function to maintain adequate levels of free nitrogenous bases for cellular function. The two highly homologous isozymes display distinct specificities toward nucleoside substrates, and both lack the amino acids employed for activation of the leaving group in the hydrolytic reaction by the NHs characterized thus far. We determined the high-resolution crystal structures of the purine- and pyrimidine-specific NHs from S. solfataricus to reveal that both enzymes belong to NH structural homology group I, despite the different substrate specificities. A Na(+) ion is bound at the active site of the pyrimidine-specific NH instead of the prototypical Ca(2+), delineating a role of the metals in the catalytic mechanism of NHs in the substrate binding rather than nucleophile activation. A conserved His residue, which regulates product release in other homologous NHs, provides crucial interactions for leaving group activation in the archaeal isozymes. Modeling of the enzyme-substrate interactions suggests that steric exclusion and catalytic selection underlie the orthogonal base specificity of the two isozymes.

  • Organizational Affiliation

    Biocrystallography Unit, Department of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, via Olgettina 58, 20132 Milan, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleosidase, (IunH-1)311Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: iunH-1SSO0505
Find proteins for Q97ZS5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97ZS5 
Go to UniProtKB:  Q97ZS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97ZS5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.94α = 90
b = 194.94β = 90
c = 42.86γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description