2ys6: Difference between revisions

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-{{Seed}}
-[[Image:2ys6.png|left|200px]]
-<!--
+==Crystal structure of GAR synthetase from Geobacillus kaustophilus==
-The line below this paragraph, containing "STRUCTURE_2ys6", creates the "Structure Box" on the page.
+<StructureSection load='2ys6' size='340' side='right'caption='[[2ys6]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_2ys6|  PDB=2ys6  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5L3C7_GEOKA Q5L3C7_GEOKA]
+== 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/ys/2ys6_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=2ys6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal structure of GAR synthetase from Geobacillus kaustophilus===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20716513}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ys6" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20716513 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20716513}}
+__TOC__
+</StructureSection>
-==About this Structure==
-YS6 is a 1 chain structure with 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].
-==Reference==
-<ref group="xtra">PMID:20716513</ref><references group="xtra"/>
 [[Category: Geobacillus kaustophilus]]
-[[Category: Phosphoribosylamine--glycine ligase]]
+[[Category: Large Structures]]
-[[Category: Baba, S.]]
+[[Category: Baba S]]
-[[Category: Kanagawa, M.]]
+[[Category: Kanagawa M]]
-[[Category: Kawai, G.]]
+[[Category: Kawai G]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kuramitsu S]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sampei G]]
-[[Category: Sampei, G.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: Atp binding]]
-[[Category: Gar synthetase]]
-[[Category: Glycinamide ribonucleotide synthetase]]
-[[Category: Ligase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Purine nucleotide biosynthetic pathway]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  8 11:19:41 2010''