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2ys6

From Proteopedia

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{{Seed}}
 
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[[Image:2ys6.png|left|200px]]
 
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==Crystal structure of GAR synthetase from Geobacillus kaustophilus==
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The line below this paragraph, containing "STRUCTURE_2ys6", creates the "Structure Box" on the page.
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<StructureSection load='2ys6' size='340' side='right'caption='[[2ys6]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2ys6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YS6 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.21&#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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
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{{STRUCTURE_2ys6| PDB=2ys6 | SCENE= }}
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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=2ys6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ys6 OCA], [https://pdbe.org/2ys6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ys6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ys6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ys6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2ys6 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q5L3C7_GEOKA Q5L3C7_GEOKA]
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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/ys/2ys6_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2ys6 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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Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the beta- and gamma- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.
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===Crystal structure of GAR synthetase from Geobacillus kaustophilus===
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Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.,Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G J Biochem. 2010 Oct;148(4):429-38. Epub 2010 Aug 16. PMID:20716513<ref>PMID:20716513</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==About this Structure==
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</div>
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2YS6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YS6 OCA].
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<div class="pdbe-citations 2ys6" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Geobacillus kaustophilus]]
[[Category: Geobacillus kaustophilus]]
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[[Category: Phosphoribosylamine--glycine ligase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Baba S]]
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[[Category: Baba, S.]]
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[[Category: Kanagawa M]]
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[[Category: Kanagawa, M.]]
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[[Category: Kawai G]]
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[[Category: Kawai, G.]]
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[[Category: Kuramitsu S]]
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[[Category: Kuramitsu, S.]]
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[[Category: Sampei G]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Sampei, G.]]
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[[Category: Yokoyama, S.]]
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[[Category: Atp binding]]
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[[Category: Gar synthetase]]
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[[Category: Glycinamide ribonucleotide synthetase]]
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[[Category: Ligase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Purine nucleotide biosynthetic pathway]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 29 03:14:10 2008''
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Current revision

Crystal structure of GAR synthetase from Geobacillus kaustophilus

PDB ID 2ys6

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