Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.19 kDa 
• Atom Count: 10851 
• Modelled Residue Count: 1224 
• Deposited Residue Count: 1224 
• Unique protein chains: 1

3T8I

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

• DOI: 10.2210/pdb3T8I/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2012-05-16 
• Deposition Author(s): Minici, C., Cacciapuoti, G., De Leo, E., Porcelli, M., Degano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

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

• PubMed: 22551416 
• DOI: 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.

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Related Citations: 

• Biochemical characterization and homology modeling of a purine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus: insights into mechanisms of protein stabilization.
  Porcelli, M., Peluso, I., Marabotti, A., Facchiano, A., Cacciapuoti, G.
  (2009) Arch Biochem Biophys 483: 55

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleosidase, (IunH-2)	A, B, C, D	306	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: iunH-2, SSO2243 EC: 3.2.2.1
Find proteins for Q97WH6 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97WH6  Go to UniProtKB:  Q97WH6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	EA [auth D], Y [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	BA [auth D],  CA [auth D],  DA [auth D],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  V [auth C],  W [auth C],  X [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], T [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	AA [auth D], E [auth A], L [auth B], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.76	α = 90
b = 81.13	β = 100.7
c = 98.02	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-01 
• Released Date: 2012-05-16 
Deposition Author(s): Minici, C., Cacciapuoti, G., De Leo, E., Porcelli, M., Degano, M.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references