3a11
From Proteopedia
(Difference between revisions)
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<StructureSection load='3a11' size='340' side='right'caption='[[3a11]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='3a11' size='340' side='right'caption='[[3a11]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3a11]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[3a11]] is a 6 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3A11 FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=3a11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a11 OCA], [https://pdbe.org/3a11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a11 RCSB], [https://www.ebi.ac.uk/pdbsum/3a11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a11 ProSAT]</span></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=3a11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a11 OCA], [https://pdbe.org/3a11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a11 RCSB], [https://www.ebi.ac.uk/pdbsum/3a11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a11 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/R15PI_THEKO R15PI_THEKO] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Only accepts the alpha-anomer of D-ribose 1,5-bisphosphate as substrate, being inactive on the beta-anomer. Displays a strict substrate specificity, since other phosphorylated sugars such as R5P, ribose, G16P, G6P, G1P, FBP, F6P, and PRPP, are not substrates. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO.<ref>PMID:17303759</ref> <ref>PMID:22511789</ref> <ref>PMID:23065974</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=3a11 ConSurf]. | </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=3a11 ConSurf]. | ||
<div style="clear:both"></div> | <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. | ||
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| - | 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> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 3a11" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Atomi | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Fujihashi | + | [[Category: Atomi H]] |
| - | [[Category: Imanaka | + | [[Category: Fujihashi M]] |
| - | [[Category: Miki | + | [[Category: Imanaka T]] |
| - | [[Category: Nakamura | + | [[Category: Miki K]] |
| - | [[Category: Nishiba | + | [[Category: Nakamura A]] |
| - | [[Category: Yano | + | [[Category: Nishiba Y]] |
| - | [[Category: Yoshida | + | [[Category: Yano A]] |
| - | + | [[Category: Yoshida S]] | |
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Current revision
Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1
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