9VTK

Structure of the family PL40 Ulvan Lyase Uly1040

Summary for 9VTK

• Entry DOI: 10.2210/pdb9vtk/pdb
• Descriptor: Uly1040, GLYCEROL, FE (III) ION, ... (7 entities in total)
• Functional Keywords: polysaccharide lyase, family pl40 ulvan lyase, lyase
• Biological source: Alteromonas macleodii
• Total number of polymer chains: 1
• Total formula weight: 97823.89

Authors

Wang, H.Q.,Suo, C.L.,Wang, P. (deposition date: 2025-07-10, release date: 2025-12-24, Last modification date: 2026-07-08)

Primary citation

Wang, H.-.Q.,Suo, C.-.L.,Liu, D.,Wang, M.-.Q.,Li, J.-.X.,Cao, H.-.Y.,Qin, Q.-.L.,Zhang, Y.-.Z.,Wang, P.,Xu, F.
Structural and functional insights into Uly1040, an ulvan lyase from polysaccharide lyase family 40.
Appl.Environ.Microbiol., 92:e0210125-e0210125, 2026

PubMed Abstract: Ulvan is a major polysaccharide in marine green algae. Its oligosaccharide degradation products possess diverse bioactivities and hold considerable potential for various applications. Ulvan lyases, the key enzymes responsible for cleaving ulvan glycosidic bonds, generate bioactive oligosaccharides and play an essential role in ulvan degradation. However, studies on ulvan lyases remain limited, particularly for the poorly characterized polysaccharide lyase (PL) 40 family. Here, we identified Uly1040, a novel PL40 ulvan lyase, from the marine bacterium isolated from the intestine of an sea slug. Uly1040 displays a unique two-domain architecture not previously reported in ulvan lyases. Mechanistically, Uly1040 employs a distinct His/Tyr catalytic strategy, divergent from known ulvan lyase mechanisms. During catalysis, Trp246 and Asn245 neutralize the negative charge of the carboxyl group at the +1 subsite. Concurrently, Mn, His487, and Asp358 activate His485 to serve as the catalytic base, while Tyr305 functions as the catalytic acid. Bioinformatic, phylogenetic, and biogeographic analyses further demonstrated that this catalytic mechanism is conserved across PL40 lyases and that Uly1040-like enzymes are widespread in marine environments. Collectively, these findings expand our understanding of PL40 ulvan lyases and provide new insights into the enzymatic basis of marine biomass utilization.

PubMed: 41532755
DOI: 10.1128/aem.02101-25

Experimental method

X-RAY DIFFRACTION (1.74 Å)