PDBsum entry 2c5e

Isomerase

PDB id: 2c5e

Contents

Protein chains

363 a.a. *

Ligands

GDD ×2

FMT ×10

NAD ×2

Waters ×870

* Residue conservation analysis

PDB id:

2c5e

Name:

Isomerase

Title:

Gdp-mannose-3', 5' -epimerase (arabidopsis thaliana), k217a, with gdp- alpha-d-mannose bound in the active site.

Structure:

Gdp-mannose-3', 5'-epimerase. Chain: a, b. Synonym: gdp-man 3,5-epimerase. Engineered: yes. Mutation: yes. Other_details: gdp-alpha-d-mannose was refined using gmp (defined as gdp, modified in the cif file to remove the second phosphate group) and mannose-monophosphate (ma7), linking the gdp o3a to the ma7 pb

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: rosetta.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.70Å R-factor: 0.134 R-free: 0.193

Authors:

L.L.Major,B.A.Wolucka,J.H.Naismith

Key ref:

L.L.Major et al. (2005). 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. PubMed id: 16366586 DOI: 10.1021/ja056490i

Date:

26-Oct-05 Release date: 14-Nov-05

Protein chains

Q93VR3  (GME_ARATH) -  GDP-mannose 3,5-epimerase from Arabidopsis thaliana

Seq: 377 a.a.

Struc: 363 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.1.3.18 - GDP-mannose 3,5-epimerase.
• Reaction:
  1. GDP-alpha-D-mannose = GDP-beta-L-gulose
  2. GDP-beta-L-gulose = GDP-beta-L-galactose

GDP-mannose (Bound ligand (Het Group name = GDD) corresponds exactly) = GDP-L-galactose

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/ja056490i

J Am Chem Soc 127:18309-18320 (2005)

PubMed id: 16366586

Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.

L.L.Major, B.A.Wolucka, J.H.Naismith.

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.