3KHS
Crystal structure of grouper iridovirus purine nucleoside phosphorylase
Summary for 3KHS
| Entry DOI | 10.2210/pdb3khs/pdb |
| Descriptor | Purine nucleoside phosphorylase, PHOSPHATE ION, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total) |
| Functional Keywords | alpha-beta structure, mixed beta-barrel, hydrolase |
| Biological source | Grouper iridovirus |
| Total number of polymer chains | 4 |
| Total formula weight | 122336.33 |
| Authors | Kang, Y.N.,Zhang, Y.,Allan, P.W.,Parker, W.B.,Ting, J.W.,Chang, C.Y.,Ealick, S.E. (deposition date: 2009-10-30, release date: 2010-02-16, Last modification date: 2024-11-06) |
| Primary citation | Kang, Y.N.,Zhang, Y.,Allan, P.W.,Parker, W.B.,Ting, J.W.,Chang, C.Y.,Ealick, S.E. Structure of grouper iridovirus purine nucleoside phosphorylase Acta Crystallogr.,Sect.D, 66:155-162, 2010 Cited by PubMed Abstract: Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4 A resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6 A, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an alpha/beta structure with a nine-stranded mixed beta-barrel flanked by a total of nine alpha-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydrogen-bonding patterns of the phosphate-binding site are similar to those found in the human and bovine PNP structures. The enzymatic activity assay of givPNP on various substrates revealed that givPNP can only accept 6-oxopurine nucleosides as substrates, which is also suggested by its amino-acid composition and active-site architecture. All these results suggest that givPNP is a homologue of mammalian PNPs in terms of amino-acid sequence, molecular mass, substrate specificity and overall structure, as well as in the composition of the active site. PubMed: 20124695DOI: 10.1107/S0907444909048276 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.38 Å) |
Structure validation
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