2ip4: Difference between revisions
From Proteopedia
Jump to navigationJump to search
New page: left|200px<br /><applet load="2ip4" size="350" color="white" frame="true" align="right" spinBox="true" caption="2ip4, resolution 2.8Å" /> '''Crystal Structure of ... |
No edit summary |
||
| (14 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8== | ||
<StructureSection load='2ip4' size='340' side='right'caption='[[2ip4]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
[ | == Structural highlights == | ||
[[ | <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> | ||
[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | ||
[[ | <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> | ||
<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> | |||
[ | </table> | ||
[ | == Function == | ||
[https://www.uniprot.org/uniprot/Q5SK40_THET8 Q5SK40_THET8] | |||
== 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/ip/2ip4_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=2ip4 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®/PubMed®, 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]] | |||
Latest revision as of 08:53, 25 October 2023
Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8
| ||||||||||||
