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| | ==Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with arabinose-5-phosphate== | | ==Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with arabinose-5-phosphate== |
| - | <StructureSection load='1uj6' size='340' side='right' caption='[[1uj6]], [[Resolution|resolution]] 1.74Å' scene=''> | + | <StructureSection load='1uj6' size='340' side='right'caption='[[1uj6]], [[Resolution|resolution]] 1.74Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1uj6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UJ6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UJ6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uj6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UJ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UJ6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.74Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uj4|1uj4]], [[1uj5|1uj5]]</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=1uj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uj6 OCA], [https://pdbe.org/1uj6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uj6 RCSB], [https://www.ebi.ac.uk/pdbsum/1uj6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uj6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uj6 TOPSAN]</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-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </span></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=1uj6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uj6 OCA], [http://pdbe.org/1uj6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uj6 RCSB], [http://www.ebi.ac.uk/pdbsum/1uj6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uj6 ProSAT], [http://www.topsan.org/Proteins/RSGI/1uj6 TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPIA_THET2 RPIA_THET2]] Involved in the first step of the non-oxidative branch of the pentose phosphate pathway. It catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. Can also act on D-ribose-5-diphosphate and D-ribose-5-triphosphate as substrate.<ref>PMID:13679361</ref> | + | [https://www.uniprot.org/uniprot/RPIA_THET2 RPIA_THET2] Involved in the first step of the non-oxidative branch of the pentose phosphate pathway. It catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. Can also act on D-ribose-5-diphosphate and D-ribose-5-triphosphate as substrate.<ref>PMID:13679361</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Ribose-5-phosphate isomerase|Ribose-5-phosphate isomerase]] | + | *[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | + | [[Category: Large Structures]] |
| - | [[Category: Ribose-5-phosphate isomerase]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Ago, H]] | + | [[Category: Ago H]] |
| - | [[Category: Hamada, K]] | + | [[Category: Hamada K]] |
| - | [[Category: Kuramitsu, S]] | + | [[Category: Kuramitsu S]] |
| - | [[Category: Miyano, M]] | + | [[Category: Miyano M]] |
| - | [[Category: Nodake, Y]] | + | [[Category: Nodake Y]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Sugahara M]] |
| - | [[Category: Sugahara, M]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Enzyme-inhibitor complex]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Rsgi]]
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| Structural highlights
Function
RPIA_THET2 Involved in the first step of the non-oxidative branch of the pentose phosphate pathway. It catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. Can also act on D-ribose-5-diphosphate and D-ribose-5-triphosphate as substrate.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Ribose-5-phosphate isomerase (Rpi) acts as a key enzyme in the oxidative and reductive pentose-phosphate pathways for the conversion of ribose-5-phosphate (R5P) to ribulose-5-phosphate and vice versa. We have determined the crystal structures of Rpi from Thermus thermophilus HB8 in complex with the open chain form of the substrate R5P and the open chain form of the C2 epimeric inhibitor arabinose-5-phosphate as well as the apo form at high resolution. The crystal structures of both complexes revealed that these ring-opened epimers are bound in the active site in a mirror symmetry binding mode. The O1 atoms are stabilized by an oxyanion hole composed of the backbone amide nitrogens in the conserved motif. In the structure of the Rpi.R5P complex, the conversion moiety O1-C1-C2-O2 in cis-configuration interacts with the carboxyl oxygens of Glu-108 in a water-excluded environment. Furthermore, the C2 hydroxyl group is presumed to be highly polarized by short hydrogen bonding with the side chain of Lys-99. R5P bound as the ring-opened reaction intermediate clarified the high stereoselectivity of the catalysis and is consistent with an aldose-ketose conversion by Rpi that proceeds via a cis-enediolate intermediate.
Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi).,Hamada K, Ago H, Sugahara M, Nodake Y, Kuramitsu S, Miyano M J Biol Chem. 2003 Dec 5;278(49):49183-90. Epub 2003 Sep 17. PMID:13679361[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hamada K, Ago H, Sugahara M, Nodake Y, Kuramitsu S, Miyano M. Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi). J Biol Chem. 2003 Dec 5;278(49):49183-90. Epub 2003 Sep 17. PMID:13679361 doi:http://dx.doi.org/10.1074/jbc.M309272200
- ↑ Hamada K, Ago H, Sugahara M, Nodake Y, Kuramitsu S, Miyano M. Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi). J Biol Chem. 2003 Dec 5;278(49):49183-90. Epub 2003 Sep 17. PMID:13679361 doi:http://dx.doi.org/10.1074/jbc.M309272200
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