6DLH

Endo-fucoidan hydrolase MfFcnA4 from glycoside hydrolase family 107

Summary for 6DLH

• Entry DOI: 10.2210/pdb6dlh/pdb
• Descriptor: Alpha-1,4-endofucoidanase, 1,2-ETHANEDIOL, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: fucan, fucoidan, glycoside hydrolase, retaining mechanism, hydrolase
• Biological source: Mariniflexile fucanivorans
• Total number of polymer chains: 1
• Total formula weight: 81554.93

Authors

Vickers, C.,Abe, K.,Salama-Alber, O.,Boraston, A.B. (deposition date: 2018-06-01, release date: 2018-10-03, Last modification date: 2024-04-03)

Primary citation

Vickers, C.,Liu, F.,Abe, K.,Salama-Alber, O.,Jenkins, M.,Springate, C.M.K.,Burke, J.E.,Withers, S.G.,Boraston, A.B.
Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to alpha-l-fucosidases from GH29.
J. Biol. Chem., 293:18296-18308, 2018

PubMed Abstract: Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.

PubMed: 30282808
DOI: 10.1074/jbc.RA118.005134

Experimental method

X-RAY DIFFRACTION (2.2 Å)