2ys6: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:2ys6.jpg|left|200px]]<br /><applet load="2ys6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2ys6, resolution 2.21&Aring;" />
-'''Crystal structure of GAR synthetase from Geobacillus kaustophilus'''<br />
-==About this Structure==
+==Crystal structure of GAR synthetase from Geobacillus kaustophilus==
-YS6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus] with <scene name='pdbligand=GLY:'>GLY</scene> and <scene name='pdbligand=AMP:'>AMP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoribosylamine--glycine_ligase Phosphoribosylamine--glycine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.13 6.3.4.13] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YS6 OCA].
+<StructureSection load='2ys6' size='340' side='right'caption='[[2ys6]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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 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>
+<div class="pdbe-citations 2ys6" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus kaustophilus]]
-[[Category: Phosphoribosylamine--glycine ligase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[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: Sampei G]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Yokoyama S]]
-[[Category: Sampei, G.]]
-[[Category: Yokoyama, S.]]
-[[Category: AMP]]
-[[Category: GLY]]
-[[Category: atp binding]]
-[[Category: gar synthetase]]
-[[Category: glycinamide ribonucleotide synthetase]]
-[[Category: ligase]]
-[[Category: national project on protein structural and functional analyses]]
-[[Category: nppsfa]]
-[[Category: purine nucleotide biosynthetic pathway]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:02:45 2008''