4AK7

Crystal structure of BpGH117_E303Q in complex with neoagarobiose

Summary for 4AK7

• Entry DOI: 10.2210/pdb4ak7/pdb
• Related: 4AK5 4AK6
• Descriptor: ANHYDRO-ALPHA-L-GALACTOSIDASE, NEOAGAROBIOSE, CALCIUM ION, ... (8 entities in total)
• Functional Keywords: hydrolase, marine glycoside hydrolase, marine polysaccharide degradation, marine cazymes, agar metabolism, seaweed biofuels
• Biological source: BACTEROIDES PLEBEIUS
• Total number of polymer chains: 2
• Total formula weight: 92919.80

Authors

Hehemann, J.H.,Smyth, L.,Yadav, A.,Vocadlo, D.J.,Boraston, A.B. (deposition date: 2012-02-21, release date: 2012-03-14, Last modification date: 2024-05-08)

Primary citation

Hehemann, J.H.,Smyth, L.,Yadav, A.,Vocadlo, D.J.,Boraston, A.B.
Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight Into the Degradation (of a Polysaccharide from) Red Seaweeds.
J.Biol.Chem., 287:13985-, 2012

PubMed Abstract: Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating D-galactose and 3,6-anhydro-L-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds.

PubMed: 22393053
DOI: 10.1074/JBC.M112.345645

Experimental method

X-RAY DIFFRACTION (1.8 Å)