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2ip4

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[[Image:2ip4.gif|left|200px]]<br /><applet load="2ip4" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ip4, resolution 2.8&Aring;" />
 
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'''Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8'''<br />
 
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==About this Structure==
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==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8==
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2IP4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=2IP4 OCA].
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<StructureSection load='2ip4' size='340' side='right'caption='[[2ip4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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[[Category: Phosphoribosylamine--glycine ligase]]
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== Structural highlights ==
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[[Category: Single protein]]
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<table><tr><td colspan='2'>[[2ip4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IP4 FirstGlance]. <br>
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[[Category: Thermus thermophilus]]
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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]] 2.8&#8491;</td></tr>
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[[Category: Baba, S.]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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[[Category: Ebihara, A.]]
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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=2ip4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip4 OCA], [https://pdbe.org/2ip4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ip4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ip4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ip4 ProSAT], [https://www.topsan.org/Proteins/RSGI/2ip4 TOPSAN]</span></td></tr>
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[[Category: Fukai, Y.]]
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</table>
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[[Category: Ishii, T.]]
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== Function ==
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[[Category: Kanagawa, M.]]
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[https://www.uniprot.org/uniprot/Q5SK40_THET8 Q5SK40_THET8]
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[[Category: Kawai, G.]]
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== Evolutionary Conservation ==
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[[Category: Kawai, H.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Nakagawa, N.]]
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Check<jmol>
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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<jmolCheckbox>
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[[Category: Sampei, G.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/2ip4_consurf.spt"</scriptWhenChecked>
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[[Category: Yanai, H.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: SO4]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: gar synthetase]]
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</jmolCheckbox>
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[[Category: ligase]]
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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=2ip4 ConSurf].
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[[Category: national project on protein structural and functional analyses]]
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<div style="clear:both"></div>
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[[Category: nppsfa]]
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<div style="background-color:#fffaf0;">
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[[Category: purd]]
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== Publication Abstract from PubMed ==
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[[Category: purine nucleotide]]
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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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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: thermus thermophilus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:54:49 2008''
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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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</div>
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<div class="pdbe-citations 2ip4" 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>
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Baba S]]
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[[Category: Ebihara A]]
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[[Category: Fukai Y]]
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[[Category: Ishii T]]
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[[Category: Kanagawa M]]
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[[Category: Kawai G]]
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[[Category: Kawai H]]
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[[Category: Nakagawa N]]
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[[Category: Sampei G]]
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[[Category: Yanai H]]

Current revision

Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8

PDB ID 2ip4

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