2ie8: Difference between revisions

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New page: left|200px<br /><applet load="2ie8" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ie8, resolution 1.8Å" /> '''Crystal structure of ...
 
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[[Image:2ie8.gif|left|200px]]<br /><applet load="2ie8" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2ie8, resolution 1.8&Aring;" />
'''Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation'''<br />


==Overview==
==Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation==
Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes, the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP, to form 3-phosphoglycerate and ATP in the presence of magnesium. During, catalysis, a conformational change occurs that brings the N- and C-domains, of PGK closer together. Here we present the 1.8A crystal structure of, unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure, of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK, (closed conformation) revealed that the conformational change reflects a, change in the interaction between the domains. We identified Arg148 as a, key residue involved in open-to-closed transition. The open conformation, of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and, Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge, and, in ternary complex, the formation of new salt bridge between Arg60, and Asp197 stabilizes the closed conformation.
<StructureSection load='2ie8' size='340' side='right'caption='[[2ie8]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ie8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_caldophilus Thermus caldophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IE8 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]] 1.8&#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=2ie8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ie8 OCA], [https://pdbe.org/2ie8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ie8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ie8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ie8 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q08GC7_THECA Q08GC7_THECA]
== 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/ie/2ie8_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=2ie8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational change occurs that brings the N- and C-domains of PGK closer together. Here we present the 1.8A crystal structure of unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK (closed conformation) revealed that the conformational change reflects a change in the interaction between the domains. We identified Arg148 as a key residue involved in open-to-closed transition. The open conformation of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation.


==About this Structure==
Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation.,Lee JH, Im YJ, Bae J, Kim D, Kim MK, Kang GB, Lee DS, Eom SH Biochem Biophys Res Commun. 2006 Dec 1;350(4):1044-9. Epub 2006 Oct 6. PMID:17045964<ref>PMID:17045964</ref>
2IE8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_caldophilus Thermus caldophilus]. Active as [http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IE8 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation., Lee JH, Im YJ, Bae J, Kim D, Kim MK, Kang GB, Lee DS, Eom SH, Biochem Biophys Res Commun. 2006 Dec 1;350(4):1044-9. Epub 2006 Oct 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17045964 17045964]
</div>
[[Category: Phosphoglycerate kinase]]
<div class="pdbe-citations 2ie8" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
 
==See Also==
*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus caldophilus]]
[[Category: Thermus caldophilus]]
[[Category: Eom, S.H.]]
[[Category: Eom SH]]
[[Category: Im, Y.J.]]
[[Category: Im YJ]]
[[Category: Lee, J.H.]]
[[Category: Lee JH]]
[[Category: crystal structure]]
[[Category: domain movement]]
[[Category: phosphoglycerate kinase]]
[[Category: thermus caldophilus]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:16:33 2007''

Latest revision as of 08:53, 25 October 2023

Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

2ie8, resolution 1.80Å

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