7JWF

Crystal structure of PdGH110B D344N in complex with alpha-(1,3)-galactobiose

Summary for 7JWF

• Entry DOI: 10.2210/pdb7jwf/pdb
• Related: 7JW4
• Descriptor: Glycoside hydrolase family 110, MALONIC ACID, MALONATE ION, ... (13 entities in total)
• Functional Keywords: beta helix, hydrolase
• Biological source: Pseudoalteromonas distincta
• Total number of polymer chains: 4
• Total formula weight: 300897.87

Authors

Hettle, A.G.,Boraston, A.B. (deposition date: 2020-08-25, release date: 2020-11-04, Last modification date: 2023-10-18)

Primary citation

McGuire, B.E.,Hettle, A.G.,Vickers, C.,King, D.T.,Vocadlo, D.J.,Boraston, A.B.
The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens.
J.Biol.Chem., 295:18426-18435, 2020

PubMed Abstract: α-Linked galactose is a common carbohydrate motif in nature that is processed by a variety of glycoside hydrolases from different families. Terminal Galα1-3Gal motifs are found as a defining feature of different blood group and tissue antigens, as well as the building block of the marine algal galactan λ-carrageenan. The blood group B antigen and linear α-Gal epitope can be processed by glycoside hydrolases in family GH110, whereas the presence of genes encoding GH110 enzymes in polysaccharide utilization loci from marine bacteria suggests a role in processing λ-carrageenan. However, the structure-function relationships underpinning the α-1,3-galactosidase activity within family GH110 remain unknown. Here we focus on a GH110 enzyme (PdGH110B) from the carrageenolytic marine bacterium U2A. We showed that the enzyme was active on Galα1-3Gal but not the blood group B antigen. X-ray crystal structures in complex with galactose and unhydrolyzed Galα1-3Gal revealed the parallel β-helix fold of the enzyme and the structural basis of its inverting catalytic mechanism. Moreover, an examination of the active site reveals likely adaptations that allow accommodation of fucose in blood group B active GH110 enzymes or, in the case of PdGH110, accommodation of the sulfate groups found on λ-carrageenan. Overall, this work provides insight into the first member of a predominantly marine clade of GH110 enzymes while also illuminating the structural basis of α-1,3-galactoside processing by the family as a whole.

PubMed: 33127644
DOI: 10.1074/jbc.RA120.015776

Experimental method

X-RAY DIFFRACTION (2.187 Å)