Structural insights into a novel Ca2+-independent PL-6 alginate lyase from Vibrio OU02 identify the possible subsites responsible for product distribution

• Published in: Biochimica et biophysica acta. General subjects Vol. 1863; no. 7; pp. 1167 - 1176
• Main Authors: Lyu, Qianqian, Zhang, Keke, Shi, Yanhong, Li, Weihua, Diao, Xiaotong, Liu, Weizhi
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.07.2019
• Subjects: Alginate lyase; alginates; biotransformation; Catalytic mechanism; industrial applications; medical treatment; mutagenesis; PL-6; Product distribution; trisaccharides; Vibrio; X-ray crystallography; PL-6; X-ray crystallography; Alginate lyase; Catalytic mechanism; Product distribution
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2019.04.013

Alginate lyases have a wide range of industrial applications, such as oligosaccharide preparation, medical treatment, and bioconversion. Therefore, the discovery and characterization of novel alginate lyases are extremely important. PL-6 alginate lyases are classified into two groups: those with a single domain or two domains. However, only one structure of a two-domain alginate lyase has been determined to date. In this study, we characterized a novel single-domain PL-6 alginate lyase (named AlyF). According to the biochemical analysis, AlyF possesses unique features compared with other PL-6 enzymes, including (1) a Ca2+-independent catalytic mechanism and (2) a PolyG-specific cleavage specificity that predominantly produces trisaccharides. The structures of AlyF and its complexes described here reveal the structural basis for these unique features and substrate binding mechanisms, which were further confirmed using mutagenesis. More importantly, we determined the possible subsites specifying the predominantly trisaccharide products of AlyF, which may facilitate the rational design of AlyF for potential applications in preparing a single alginate oligomer. •A novel Ca2+-independent PL-6 alginate lyase, AlyF, was characterized.•The first structure of a single-domain PL-6 alginate lyase was solved.•Instead of Ca2+, a water involved in the catalytic mechanism of AlyF.•The possible subsite responsible for the product distribution was identified by structure-based rational design.