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3khs
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3khs is ON HOLD Authors: Kang, Y.N., Zhang, Y., Allan, P.W., Parker, W.B., Ting, J.W., Chang, C.Y., Ealick, S.E. Description: Crystal structure of ...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of grouper iridovirus purine nucleoside phosphorylase== | |
| + | <StructureSection load='3khs' size='340' side='right'caption='[[3khs]], [[Resolution|resolution]] 2.38Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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='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='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='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> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q5YBA4_9VIRU Q5YBA4_9VIRU] | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3khs_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == 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<ref>PMID:20124695</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3khs" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Grouper iridovirus]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Allan PW]] | ||
| + | [[Category: Chang CY]] | ||
| + | [[Category: Ealick SE]] | ||
| + | [[Category: Kang YN]] | ||
| + | [[Category: Parker WB]] | ||
| + | [[Category: Ting JW]] | ||
| + | [[Category: Zhang Y]] | ||
Current revision
Crystal structure of grouper iridovirus purine nucleoside phosphorylase
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Categories: Grouper iridovirus | Large Structures | Allan PW | Chang CY | Ealick SE | Kang YN | Parker WB | Ting JW | Zhang Y
