7XZF

Wild type of the N-terminal domain of fucoidan lyase FdlA

Summary for 7XZF

• Entry DOI: 10.2210/pdb7xzf/pdb
• Descriptor: Fucoidan lyase, SULFATE ION, IMIDAZOLE, ... (5 entities in total)
• Functional Keywords: fucobacter marina, fucoidan lyase, polysaccharide lyase, lyase
• Biological source: Flavobacteriaceae bacterium SA-0082
• Total number of polymer chains: 2
• Total formula weight: 101607.70

Authors

Wang, J.,Li, M.,Pan, X. (deposition date: 2022-06-02, release date: 2022-09-28, Last modification date: 2024-05-29)

Primary citation

Wang, J.,Liu, Z.,Pan, X.,Wang, N.,Li, L.,Du, Y.,Li, J.,Li, M.
Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082.
Mar Drugs, 20:-, 2022

PubMed Abstract: Fucoidans represent a type of polyanionic fucose-containing sulfated polysaccharides (FCSPs) that are cleaved by fucoidan-degrading enzymes, producing low-molecular-weight fucoidans with multiple biological activities suitable for pharmacological use. Most of the reported fucoidan-degrading enzymes are glycoside hydrolases, which have been well studied for their structures and catalytic mechanisms. Little is known, however, about the rarer fucoidan lyases, primarily due to the lack of structural information. FdlA from sp. SA-0082 is an endo-type fucoidan-degrading enzyme that cleaves the sulfated fuco-glucuronomannan (SFGM) through a lytic mechanism. Here, we report nine crystal structures of the catalytic N-terminal domain of FdlA (FdlA-NTD), in both its wild type (WT) and mutant forms, at resolutions ranging from 1.30 to 2.25 Å. We show that the FdlA-NTD adopts a right-handed parallel β-helix fold, and possesses a substrate binding site composed of a long groove and a unique alkaline pocket. Our structural, biochemical, and enzymological analyses strongly suggest that FdlA-NTD utilizes catalytic residues different from other β-helix polysaccharide lyases, potentially representing a novel polysaccharide lyase family.

PubMed: 36005536
DOI: 10.3390/md20080533

Experimental method

X-RAY DIFFRACTION (1.3 Å)