2C54

gdp-mannose-3', 5' -epimerase (arabidopsis thaliana),k178r, with gdp-beta-l-gulose and gdp-4-keto-beta-l-gulose bound in active site.

Summary for 2C54

• Entry DOI: 10.2210/pdb2c54/pdb
• Related: 2C59 2C5A 2C5E
• Descriptor: GDP-MANNOSE-3', 5'-EPIMERASE, GUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE, GUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE, ... (7 entities in total)
• Functional Keywords: 3' 5'-epimerase, short chain dehydratase/reductase, gdp-mannose, gdp-gulose, gdp-galactose, keto intermediate, vitamin c, sdr, isomerase, ascorbate biosynthesis, nad
• Biological source: Arabidopsis thaliana (MOUSE-EAR CRESS)
• Total number of polymer chains: 2
• Total formula weight: 90754.16

Authors

Major, L.L.,Wolucka, B.A.,Naismith, J.H. (deposition date: 2005-10-25, release date: 2005-11-14, Last modification date: 2024-05-08)

Primary citation

Major, L.L.,Wolucka, B.A.,Naismith, J.H.
Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.
J. Am. Chem. Soc., 127:18309-18320, 2005

PubMed Abstract: 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.

PubMed: 16366586
DOI: 10.1021/ja056490i

Experimental method

X-RAY DIFFRACTION (1.5 Å)