5yfv: Difference between revisions
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==Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP== | ==Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP== | ||
<StructureSection load='5yfv' size='340' side='right' caption='[[5yfv]], [[Resolution|resolution]] 2.75Å' scene=''> | <StructureSection load='5yfv' size='340' side='right'caption='[[5yfv]], [[Resolution|resolution]] 2.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5yfv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YFV OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5yfv]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YFV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YFV FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0208 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yfv OCA], [http://pdbe.org/5yfv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yfv RCSB], [http://www.ebi.ac.uk/pdbsum/5yfv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yfv ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus horikoshii]] | |||
[[Category: Ribose 1,5-bisphosphate isomerase]] | [[Category: Ribose 1,5-bisphosphate isomerase]] | ||
[[Category: Gogoi, P]] | [[Category: Gogoi, P]] | ||
Revision as of 12:18, 21 October 2020
Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMPCrystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP
Structural highlights
Function[R15PI_PYRHO] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity). Publication Abstract from PubMedThe homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulatory subunits of eIF2B. However, PH0208 protein also shares sequence similarity with a functionally non-related enzyme, ribose-1,5-bisphosphate isomerase (R15Pi), involved in conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) in an AMP-dependent manner. Herein, we have determined the crystal structure of PH0208 protein in order to decipher its true function. Although structurally similar to the regulatory subunits of eIF2B, the ability to bind R15P and RuBP suggests that PH0208 would function as R15Pi. Additionally, this study for the first time reports the binding sites of AMP and GMP in R15Pi. The AMP binding site in PH0208 protein clarified the role of AMP in providing structural stability to R15Pi. The binding of GMP to the 'AMP binding site' in addition to its own binding site indicates that GMP might also execute a similar function, though with less specificity. Furthermore, we have utilized the resemblance between PH0208 and the regulatory subunits of eIF2B to propose a model for the regulatory mechanism of eIF2B in eukaryotes. A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.,Gogoi P, Kanaujia SP Sci Rep. 2018 Jan 30;8(1):1891. doi: 10.1038/s41598-018-20418-w. PMID:29382938[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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