7X7W

The X-ray Crystallographic Structure of D-Psicose 3-epimerase from Clostridia bacterium

Summary for 7X7W

• Entry DOI: 10.2210/pdb7x7w/pdb
• Descriptor: D-PSICOSE 3-EPIMERASE, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: d-psicose 3-epimerase, isomerase
• Biological source: Clostridia bacterium
• Total number of polymer chains: 2
• Total formula weight: 64806.95

Authors

Li, Z.F.,Ban, X.F.,Xie, X.F.,Tian, Y.X.,Li, C.M.,Gu, Z.B. (deposition date: 2022-03-10, release date: 2022-09-07, Last modification date: 2025-08-06)

Primary citation

Xie, X.,Tian, Y.,Ban, X.,Li, C.,Yang, H.,Li, Z.
Crystal structure of a novel homodimeric D-allulose 3-epimerase from a Clostridia bacterium.
Acta Crystallogr D Struct Biol, 78:1180-1191, 2022

PubMed Abstract: D-Allulose, a low-calorie rare sugar with various physiological functions, is mainly produced through the isomerization of D-fructose by ketose 3-epimerases (KEases), which exhibit various substrate specificities. A novel KEase from a Clostridia bacterium (CDAE) was identified to be a D-allulose 3-epimerase and was further characterized as thermostable and metal-dependent. In order to explore its structure-function relationship, the crystal structure of CDAE was determined using X-ray diffraction at 2.10 Å resolution, revealing a homodimeric D-allulose 3-epimerase structure with extensive interactions formed at the dimeric interface that contribute to structure stability. Structural analysis identified the structural features of CDAE, which displays a common (β/α)-TIM barrel and an ordered Mn-binding architecture at the active center, which may explain the positive effects of Mn on the activity and stability of CDAE. Furthermore, comparison of CDAE and other KEase structures revealed several structural differences, highlighting the remarkable differences in enzyme-substrate binding at the O4, O5 and O6 sites of the bound substrate, which are mainly induced by distinct hydrophobic pockets in the active center. The shape and hydrophobicity of this pocket appear to produce the differences in specificity and affinity for substrates among KEase family enzymes. Exploration of the crystal structure of CDAE provides a better understanding of its structure-function relationship, which might provide a basis for molecular modification of CDAE and further provides a reference for other KEases.

PubMed: 36048157
DOI: 10.1107/S2059798322007707

Experimental method

X-RAY DIFFRACTION (2.097 Å)