2QUM

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii with D-tagatose

Summary for 2QUM

• Entry DOI: 10.2210/pdb2qum/pdb
• Related: 2QUL 2QUN
• Descriptor: D-tagatose 3-epimerase, D-tagatose, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: beta/alpha barrel, isomerase
• Biological source: Pseudomonas cichorii
• Total number of polymer chains: 4
• Total formula weight: 131569.99

Authors

Yoshida, H.,Yamada, M.,Nishitani, T.,Takada, G.,Izumori, K.,Kamitori, S. (deposition date: 2007-08-06, release date: 2007-12-25, Last modification date: 2023-10-25)

Primary citation

Yoshida, H.,Yamada, M.,Nishitani, T.,Takada, G.,Izumori, K.,Kamitori, S.
Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose
J.Mol.Biol., 374:443-453, 2007

PubMed Abstract: Pseudomonas cichoriiid-tagatose 3-epimerase (P. cichoriid-TE) can efficiently catalyze the epimerization of not only d-tagatose to d-sorbose, but also d-fructose to d-psicose, and is used for the production of d-psicose from d-fructose. The crystal structures of P. cichoriid-TE alone and in complexes with d-tagatose and d-fructose were determined at resolutions of 1.79, 2.28, and 2.06 A, respectively. A subunit of P. cichoriid-TE adopts a (beta/alpha)(8) barrel structure, and a metal ion (Mn(2+)) found in the active site is coordinated by Glu152, Asp185, His211, and Glu246 at the end of the beta-barrel. P. cichoriid-TE forms a stable dimer to give a favorable accessible surface for substrate binding on the front side of the dimer. The simulated omit map indicates that O2 and O3 of d-tagatose and/or d-fructose coordinate Mn(2+), and that C3-O3 is located between carboxyl groups of Glu152 and Glu246, supporting the previously proposed mechanism of deprotonation/protonation at C3 by two Glu residues. Although the electron density is poor at the 4-, 5-, and 6-positions of the substrates, substrate-enzyme interactions can be deduced from the significant electron density at O6. The O6 possibly interacts with Cys66 via hydrogen bonding, whereas O4 and O5 in d-tagatose and O4 in d-fructose do not undergo hydrogen bonding to the enzyme and are in a hydrophobic environment created by Phe7, Trp15, Trp113, and Phe248. Due to the lack of specific interactions between the enzyme and its substrates at the 4- and 5-positions, P. cichoriid-TE loosely recognizes substrates in this region, allowing it to efficiently catalyze the epimerization of d-tagatose and d-fructose (C4 epimer of d-tagatose) as well. Furthermore, a C3-O3 proton-exchange mechanism for P. cichoriid-TE is suggested by X-ray structural analysis, providing a clear explanation for the regulation of the ionization state of Glu152 and Glu246.

PubMed: 17936787
DOI: 10.1016/j.jmb.2007.09.033

Experimental method

X-RAY DIFFRACTION (2.28 Å)