3a11: Difference between revisions
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==Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1== | |||
=== | <StructureSection load='3a11' size='340' side='right' caption='[[3a11]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3a11]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis_kod1 Thermococcus kodakarensis kod1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A11 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E2b2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Thermococcus kodakarensis KOD1])</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3a11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a11 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a11 RCSB], [http://www.ebi.ac.uk/pdbsum/3a11 PDBsum]</span></td></tr> | |||
</table> | |||
== 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/a1/3a11_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribose-1,5-bisphosphate isomerase (R15Pi) is a novel enzyme recently identified as a member of an AMP metabolic pathway in archaea. The enzyme converts D-ribose 1,5-bisphosphate (R15P) into ribulose 1,5-bisphosphate (RuBP), providing the substrate for archaeal ribulose-1,5-bisphosphate carboxylase/oxygenases. We here report the crystal structures of R15Pi from Thermococcus kodakarensis KOD1 (Tk-R15Pi) with and without its substrate or product. Tk-R15Pi is a hexameric enzyme formed by the trimerization of dimer units. Biochemical analyses show that Tk-R15Pi only accepts the alpha-anomer of R15P and that Cys133 and Asp202 residues are essential for RuBP production. Comparison of the determined structures reveals that the unliganded and product-binding structures are in an open form, whereas the substrate-binding structure adopts a closed form, indicating domain movement upon substrate binding. The conformational change to the closed form optimizes active-site configuration and also isolates the active site from the solvent, which may allow deprotonation of Cys133 and protonation of Asp202 to occur. The structural features of the substrate-binding form and biochemical evidence lead us to propose that the isomerase reaction proceeds via a cis-phosphoenolate intermediate. | |||
Dynamic, ligand-dependent conformational change triggers the reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.,Nakamura A, Fujihashi M, Aono R, Sato T, Nishiba Y, Yoshida S, Yano A, Atomi H, Imanaka T, Miki K J Biol Chem. 2012 Apr 17. PMID:22511789<ref>PMID:22511789</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Thermococcus kodakarensis kod1]] | [[Category: Thermococcus kodakarensis kod1]] | ||
[[Category: Atomi, H | [[Category: Atomi, H]] | ||
[[Category: Fujihashi, M | [[Category: Fujihashi, M]] | ||
[[Category: Imanaka, T | [[Category: Imanaka, T]] | ||
[[Category: Miki, K | [[Category: Miki, K]] | ||
[[Category: Nakamura, A | [[Category: Nakamura, A]] | ||
[[Category: Nishiba, Y | [[Category: Nishiba, Y]] | ||
[[Category: Yano, A | [[Category: Yano, A]] | ||
[[Category: Yoshida, S | [[Category: Yoshida, S]] | ||
[[Category: Hexamer]] | [[Category: Hexamer]] | ||
[[Category: Initiation factor]] | [[Category: Initiation factor]] | ||
[[Category: Isomerase]] | [[Category: Isomerase]] | ||
[[Category: Rossmann fold]] | [[Category: Rossmann fold]] | ||
Revision as of 13:48, 18 December 2014
Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1
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