3T8J

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

Summary for 3T8J

• Entry DOI: 10.2210/pdb3t8j/pdb
• Related: 1Q8F 2MAS 3G5I
• Descriptor: Purine nucleosidase, (IunH-1), SODIUM ION (3 entities in total)
• Functional Keywords: nucleoside hydrolase, thermostable protein, open (alpha, beta) structure, rossmann fold, nh-fold, nucleotide metabolism, n-glycosidase, hydrolase
• Biological source: Sulfolobus solfataricus
• Total number of polymer chains: 1
• Total formula weight: 35272.38

Authors

Minici, C.,Cacciapuoti, G.,De Leo, E.,Porcelli, M.,Degano, M. (deposition date: 2011-08-01, release date: 2012-05-16, Last modification date: 2023-09-13)

Primary citation

Minici, C.,Cacciapuoti, G.,De Leo, E.,Porcelli, M.,Degano, M.
New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases from the Structures of Two Isozymes from Sulfolobus solfataricus.
Biochemistry, 51:4590-4599, 2012

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.

PubMed: 22551416
DOI: 10.1021/bi300209g

Experimental method

X-RAY DIFFRACTION (1.6 Å)