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| | ==Crystal structure of grouper iridovirus purine nucleoside phosphorylase== | | ==Crystal structure of grouper iridovirus purine nucleoside phosphorylase== |
| - | <StructureSection load='3khs' size='340' side='right' caption='[[3khs]], [[Resolution|resolution]] 2.38Å' scene=''> | + | <StructureSection load='3khs' size='340' side='right'caption='[[3khs]], [[Resolution|resolution]] 2.38Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3khs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Grouper_iridovirus Grouper iridovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KHS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3khs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Grouper_iridovirus Grouper iridovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KHS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GIV43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=127569 Grouper iridovirus])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3khs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khs OCA], [https://pdbe.org/3khs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3khs RCSB], [https://www.ebi.ac.uk/pdbsum/3khs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3khs ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3khs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3khs OCA], [http://pdbe.org/3khs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3khs RCSB], [http://www.ebi.ac.uk/pdbsum/3khs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3khs ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5YBA4_9VIRU Q5YBA4_9VIRU] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Purine nucleoside phosphorylase|Purine nucleoside phosphorylase]] | + | *[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Grouper iridovirus]] | | [[Category: Grouper iridovirus]] |
| - | [[Category: Purine-nucleoside phosphorylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Allan, P W]] | + | [[Category: Allan PW]] |
| - | [[Category: Chang, C Y]] | + | [[Category: Chang CY]] |
| - | [[Category: Ealick, S E]] | + | [[Category: Ealick SE]] |
| - | [[Category: Kang, Y N]] | + | [[Category: Kang YN]] |
| - | [[Category: Parker, W B]] | + | [[Category: Parker WB]] |
| - | [[Category: Ting, J W]] | + | [[Category: Ting JW]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Zhang Y]] |
| - | [[Category: Alpha-beta structure]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mixed beta-barrel]]
| + | |
| Structural highlights
Function
Q5YBA4_9VIRU
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Structure of grouper iridovirus purine nucleoside phosphorylase.,Kang YN, Zhang Y, Allan PW, Parker WB, Ting JW, Chang CY, Ealick SE Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):155-62. Epub 2010, Jan 22. PMID:20124695[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kang YN, Zhang Y, Allan PW, Parker WB, Ting JW, Chang CY, Ealick SE. Structure of grouper iridovirus purine nucleoside phosphorylase. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):155-62. Epub 2010, Jan 22. PMID:20124695 doi:10.1107/S0907444909048276
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