2yya: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2yya.png|left|200px]]


<!--
==Crystal structure of GAR synthetase from Aquifex aeolicus==
The line below this paragraph, containing "STRUCTURE_2yya", creates the "Structure Box" on the page.
<StructureSection load='2yya' size='340' side='right'caption='[[2yya]], [[Resolution|resolution]] 2.40&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'>[[2yya]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YYA 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]] 2.4&#8491;</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=2yya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yya OCA], [https://pdbe.org/2yya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yya RCSB], [https://www.ebi.ac.uk/pdbsum/2yya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yya ProSAT], [https://www.topsan.org/Proteins/RSGI/2yya TOPSAN]</span></td></tr>
{{STRUCTURE_2yya|  PDB=2yya  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/PUR2_AQUAE PUR2_AQUAE]
== 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/yy/2yya_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2yya 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 Aquifex aeolicus===
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>
==About this Structure==
</div>
2YYA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YYA OCA].
<div class="pdbe-citations 2yya" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[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: 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 Sun Sep 28 23:17:56 2008''

Latest revision as of 08:08, 23 October 2024

Crystal structure of GAR synthetase from Aquifex aeolicus

2yya, resolution 2.40Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=2yya&oldid=4235185"