2HK1

Crystal structure of D-psicose 3-epimerase (DPEase) in the presence of D-fructose

Summary for 2HK1

• Entry DOI: 10.2210/pdb2hk1/pdb
• Related: 2HK0
• Descriptor: D-PSICOSE 3-EPIMERASE, D-fructose, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: tim-barrel, isomerase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 4
• Total formula weight: 137781.58

Authors

Kim, K.,Kim, H.J.,Oh, D.K.,Cha, S.S.,Rhee, S. (deposition date: 2006-07-03, release date: 2006-08-29, Last modification date: 2024-11-06)

Primary citation

Kim, K.,Kim, H.J.,Oh, D.K.,Cha, S.S.,Rhee, S.
Crystal Structure of d-Psicose 3-epimerase from Agrobacterium tumefaciens and its Complex with True Substrate d-Fructose: A Pivotal Role of Metal in Catalysis, an Active Site for the Non-phosphorylated Substrate, and its Conformational Changes
J.Mol.Biol., 361:920-931, 2006

PubMed Abstract: D-psicose, a rare sugar produced by the enzymatic reaction of D-tagatose 3-epimerase (DTEase), has been used extensively for the bioproduction of various rare carbohydrates. Recently characterized D-psicose 3-epimerase (DPEase) from Agrobacterium tumefaciens was found to belong to the DTEase family and to catalyze the interconversion of D-fructose and D-psicose by epimerizing the C-3 position, with marked efficiency for D-psicose. The crystal structures of DPEase and its complex with the true substrate D-fructose were determined; DPEase is a tetramer and each monomer belongs to a TIM-barrel fold. The active site in each subunit is distinct from that of other TIM-barrel enzymes, which use phosphorylated ligands as the substrate. It contains a metal ion with octahedral coordination to two water molecules and four residues that are absolutely conserved across the DTEase family. Upon binding of D-fructose, the substrate displaces water molecules in the active site, with a conformation mimicking the intermediate cis-enediolate. Subsequently, Trp112 and Pro113 in the beta4-alpha4 loop undergo significant structural changes, sealing off the active site. Structural evidence and site-directed mutagenesis of the putative catalytic residues suggest that the metal ion plays a pivotal role in catalysis by anchoring the bound D-fructose, and Glu150 and Glu244 carry out an epimerization reaction at the C-3 position.

PubMed: 16876192
DOI: 10.1016/j.jmb.2006.06.069

Experimental method

X-RAY DIFFRACTION (2.3 Å)