1uj4: Difference between revisions
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==Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase== | |||
<StructureSection load='1uj4' size='340' side='right'caption='[[1uj4]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1uj4]] 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=1UJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UJ4 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1uj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uj4 OCA], [https://pdbe.org/1uj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1uj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uj4 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uj4 TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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 == | |||
[[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/uj/1uj4_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1uj4 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:13679361</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1uj4" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
[[ | *[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
[[Category: Ago | [[Category: Ago H]] | ||
[[Category: Hamada | [[Category: Hamada K]] | ||
[[Category: Kuramitsu | [[Category: Kuramitsu S]] | ||
[[Category: Miyano | [[Category: Miyano M]] | ||
[[Category: Nodake | [[Category: Nodake Y]] | ||
[[Category: Sugahara M]] | |||
[[Category: Sugahara | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | |||
Latest revision as of 10:38, 23 October 2024
Crystal structure of Thermus thermophilus ribose-5-phosphate isomeraseCrystal structure of Thermus thermophilus ribose-5-phosphate isomerase
Structural highlights
FunctionRPIA_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 PubMedRibose-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 AlsoReferences
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