2c54: Difference between revisions
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==gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.== | ==gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.== | ||
<StructureSection load='2c54' size='340' side='right' caption='[[2c54]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='2c54' size='340' side='right'caption='[[2c54]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2c54]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C54 OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[2c54]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C54 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2C54 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GKD:GUANOSINE+5-DIPHOSPHATE-4-KETO-BETA-L-GULOSE'>GKD</scene>, <scene name='pdbligand=GKE:GUANOSINE+5-DIPHOSPHATE-BETA-L-GULOSE'>GKE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GKD:GUANOSINE+5-DIPHOSPHATE-4-KETO-BETA-L-GULOSE'>GKD</scene>, <scene name='pdbligand=GKE:GUANOSINE+5-DIPHOSPHATE-BETA-L-GULOSE'>GKE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c59|2c59]], [[2c5a|2c5a]], [[2c5e|2c5e]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c59|2c59]], [[2c5a|2c5a]], [[2c5e|2c5e]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/GDP-mannose_3,5-epimerase GDP-mannose 3,5-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.18 5.1.3.18] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/GDP-mannose_3,5-epimerase GDP-mannose 3,5-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.18 5.1.3.18] </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=2c54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c54 OCA], [http://pdbe.org/2c54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c54 RCSB], [http://www.ebi.ac.uk/pdbsum/2c54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c54 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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[[Category: Arath]] | [[Category: Arath]] | ||
[[Category: GDP-mannose 3,5-epimerase]] | [[Category: GDP-mannose 3,5-epimerase]] | ||
[[Category: Large Structures]] | |||
[[Category: Major, L L]] | [[Category: Major, L L]] | ||
[[Category: Naismith, J H]] | [[Category: Naismith, J H]] | ||
Revision as of 10:53, 4 November 2020
gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.
Structural highlights
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 PubMedGDP-mannose-3',5'-epimerase (GME) from Arabidopsis thaliana catalyzes the epimerization of both the 3' and 5' positions of GDP-alpha-D-mannose to yield GDP-beta-L-galactose. Production of the C5' epimer of GDP-alpha-D-mannose, GDP-beta-L-gulose, has also been reported. The reaction occurs as part of vitamin C biosynthesis in plants. We have determined structures of complexes of GME with GDP-alpha-D-mannose, GDP-beta-L-galactose, and a mixture of GDP-beta-L-gulose with GDP-beta-L-4-keto-gulose to resolutions varying from 2.0 to 1.4 A. The enzyme has the classical extended short-chain dehydratase/reductase (SDR) fold. We have confirmed that GME establishes an equilibrium between two products, GDP-beta-L-galactose and GDP-beta-L-gulose. The reaction proceeds by C4' oxidation of GDP-alpha-D-mannose followed by epimerization of the C5' position to give GDP-beta-L-4-keto-gulose. This intermediate is either reduced to give GDP-beta-L-gulose or the C3' position is epimerized to give GDP-beta-L-4-keto-galactose, then C4' is reduced to GDP-beta-L-galactose. The combination of oxidation, epimerization, and reduction in a single active site is unusual. Structural analysis coupled to site-directed mutagenesis suggests C145 and K217 as the acid/base pair responsible for both epimerizations. On the basis of the structure of the GDP-beta-L-gulose/GDP-beta-L-4-keto-gulose co-complex, we predict that a ring flip occurs during the first epimerization and that a boat intermediate is likely for the second epimerization. Comparison of GME with other SDR enzymes known to abstract a protein alpha to the keto function of a carbohydrate identifies key common features. Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.,Major LL, Wolucka BA, Naismith JH J Am Chem Soc. 2005 Dec 28;127(51):18309-20. PMID:16366586[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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