2c5e
From Proteopedia
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|PDB= 2c5e |SIZE=350|CAPTION= <scene name='initialview01'>2c5e</scene>, resolution 1.700Å | |PDB= 2c5e |SIZE=350|CAPTION= <scene name='initialview01'>2c5e</scene>, resolution 1.700Å | ||
|SITE= <scene name='pdbsite=AC1:Fmt+Binding+Site+For+Chain+B'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Fmt+Binding+Site+For+Chain+B'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=GDD:GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> | + | |LIGAND= <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GDD:GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> |
| - | + | |ACTIVITY= <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> | |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5e OCA], [http://www.ebi.ac.uk/pdbsum/2c5e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c5e RCSB]</span> | ||
}} | }} | ||
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[[Category: Naismith, J H.]] | [[Category: Naismith, J H.]] | ||
[[Category: Wolucka, B A.]] | [[Category: Wolucka, B A.]] | ||
| - | [[Category: FMT]] | ||
| - | [[Category: GDD]] | ||
| - | [[Category: NAD]] | ||
[[Category: 3' 5'-epimerase]] | [[Category: 3' 5'-epimerase]] | ||
[[Category: ascorbate biosynthesis]] | [[Category: ascorbate biosynthesis]] | ||
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[[Category: vitamin c]] | [[Category: vitamin c]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:16:37 2008'' |
Revision as of 23:16, 30 March 2008
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| , resolution 1.700Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , | ||||||
| Activity: | GDP-mannose 3,5-epimerase, with EC number 5.1.3.18 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
GDP-MANNOSE-3', 5'-EPIMERASE (ARABIDOPSIS THALIANA), K217A, WITH GDP-ALPHA-D-MANNOSE BOUND IN THE ACTIVE SITE.
Overview
GDP-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.
About this Structure
2C5E is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 02:16:37 2008
