4AK5
Native crystal structure of BpGH117
Summary for 4AK5
| Entry DOI | 10.2210/pdb4ak5/pdb |
| Related | 4AK6 4AK7 |
| Descriptor | ANHYDRO-ALPHA-L-GALACTOSIDASE, CHLORIDE ION, 1,2-ETHANEDIOL, ... (5 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 | 92150.50 |
| 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 Cited by 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: 22393053DOI: 10.1074/JBC.M112.345645 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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