3vm6: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
Line 1: Line 1:
{{STRUCTURE_3vm6|  PDB=3vm6  |  SCENE=  }}
==Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate==
===Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate===
<StructureSection load='3vm6' size='340' side='right' caption='[[3vm6]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
{{ABSTRACT_PUBMED_22511789}}
== Structural highlights ==
<table><tr><td colspan='2'>[[3vm6]] is a 3 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=3VM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VM6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a11|3a11]], [[3a9c|3a9c]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E2b2, TK0185 ([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=3vm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vm6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vm6 RCSB], [http://www.ebi.ac.uk/pdbsum/3vm6 PDBsum]</span></td></tr>
</table>
<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.


==About this Structure==
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>
[[3vm6]] is a 3 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=3VM6 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<ref group="xtra">PMID:022511789</ref><references group="xtra"/><references/>
</div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Thermococcus kodakarensis kod1]]
[[Category: Thermococcus kodakarensis kod1]]
[[Category: Aono, R.]]
[[Category: Aono, R]]
[[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: Sato, T.]]
[[Category: Sato, T]]
[[Category: Yano, A.]]
[[Category: Yano, A]]
[[Category: Yoshida, S.]]
[[Category: Yoshida, S]]
[[Category: Amp metabolism]]
[[Category: Amp metabolism]]
[[Category: Hexamer]]
[[Category: Hexamer]]
Retrieved from "https://proteopedia.org/3vm6"