3khs

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{{STRUCTURE_3khs| PDB=3khs | SCENE= }}
 
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===Crystal structure of grouper iridovirus purine nucleoside phosphorylase===
 
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{{ABSTRACT_PUBMED_20124695}}
 
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==About this Structure==
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==Crystal structure of grouper iridovirus purine nucleoside phosphorylase==
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[[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].
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<StructureSection load='3khs' size='340' side='right'caption='[[3khs]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q5YBA4_9VIRU Q5YBA4_9VIRU]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khs_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3khs ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==Reference==
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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<ref>PMID:20124695</ref>
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<ref group="xtra">PMID:020124695</ref><references group="xtra"/><references/>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3khs" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Grouper iridovirus]]
[[Category: Grouper iridovirus]]
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[[Category: Purine-nucleoside phosphorylase]]
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[[Category: Large Structures]]
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[[Category: Allan, P W.]]
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[[Category: Allan PW]]
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[[Category: Chang, C Y.]]
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[[Category: Chang CY]]
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[[Category: Ealick, S E.]]
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[[Category: Ealick SE]]
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[[Category: Kang, Y N.]]
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[[Category: Kang YN]]
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[[Category: Parker, W B.]]
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[[Category: Parker WB]]
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[[Category: Ting, J W.]]
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[[Category: Ting JW]]
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[[Category: Zhang, Y.]]
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[[Category: Zhang Y]]
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[[Category: Alpha-beta structure]]
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[[Category: Hydrolase]]
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[[Category: Mixed beta-barrel]]
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Current revision

Crystal structure of grouper iridovirus purine nucleoside phosphorylase

PDB ID 3khs

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