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[[Image:2ip4.gif|left|200px]]<br /><applet load="2ip4" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2ip4, resolution 2.8&Aring;" />
'''Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8'''<br />


==About this Structure==
==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8==
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].  
<StructureSection load='2ip4' size='340' side='right'caption='[[2ip4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
[[Category: Phosphoribosylamine--glycine ligase]]
== Structural highlights ==
[[Category: Single protein]]
<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>
[[Category: Thermus thermophilus]]
</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>
[[Category: Baba, S.]]
<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>
[[Category: Ebihara, A.]]
<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>
[[Category: Fukai, Y.]]
</table>
[[Category: Ishii, T.]]
== Function ==
[[Category: Kanagawa, M.]]
[https://www.uniprot.org/uniprot/Q5SK40_THET8 Q5SK40_THET8]  
[[Category: Kawai, G.]]
== Evolutionary Conservation ==
[[Category: Kawai, H.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Nakagawa, N.]]
Check<jmol>
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
  <jmolCheckbox>
[[Category: Sampei, G.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/2ip4_consurf.spt"</scriptWhenChecked>
[[Category: Yanai, H.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: SO4]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: gar synthetase]]
  </jmolCheckbox>
[[Category: ligase]]
</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].
[[Category: national project on protein structural and functional analyses]]
<div style="clear:both"></div>
[[Category: nppsfa]]
<div style="background-color:#fffaf0;">
[[Category: purd]]
== Publication Abstract from PubMed ==
[[Category: purine nucleotide]]
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.
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: structural genomics]]
[[Category: thermus thermophilus]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:54:49 2008''
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 2ip4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Baba S]]
[[Category: Ebihara A]]
[[Category: Fukai Y]]
[[Category: Ishii T]]
[[Category: Kanagawa M]]
[[Category: Kawai G]]
[[Category: Kawai H]]
[[Category: Nakagawa N]]
[[Category: Sampei G]]
[[Category: Yanai H]]
Retrieved from "https://proteopedia.org/2ip4"