Crystal structure of a novel homodimeric d‐allulose 3‐epimerase from a Clostridia bacterium. Issue 9 (30th August 2022)

• Record Type: Journal Article
• Authors: Xie, Xiaofang; Tian, Yixiong; Ban, Xiaofeng; Li, Caiming; Yang, Hongshun; Li, Zhaofeng
• Is Part Of: Acta crystallographica. Volume 78:Issue 9(2022)
• Page Start: 1180
• Page End: 1191
• Publication Date: 2022-08-30
• Subjects: d‐allulose -- ketose 3‐epimerases -- crystal structure -- hydrophobic pocket -- Clostridia; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798322007707
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : The crystal structure of a novel homodimeric d ‐allulose 3‐epimerase provides detailed information for better understanding of its structure–function relationship and might offer a theoretical basis for industrial applications and molecular modifications. 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)8 ‐TIM barrel and an ordered Mn 2+ ‐binding architecture at the active center, which may explain the positive effects of Mn 2+ 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.