4asm | pdb_00004asm
Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans
Structural highlights
FunctionAGAD_ZOBGA Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place. Requires at least 4 consecutive agarose units and is highly intolerant to modifications.[1] Publication Abstract from PubMedZobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably this marine Bacteroidetes possesses a complex agarolytic system comprising 4 beta-agarases and 5 beta-porphyranases, all belonging to the glycoside hydrolase family 16. While beta-agarases are specific for the neutral agarobiose motives, the recently discovered beta-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here we report the biochemical and structural comparison of five beta-porphyranases and beta-agarases from Z. galactanivorans. The respective degradation patterns of two beta-porphyranases and three beta-agarases are analyzed by their action on defined hybrid oligosaccharides. In the light of the high resolution crystal structures the biochemical results allow a detailed mapping of substrate specificities along the enzymes active site groove. While PorA displays a strict requirement for C6-sulfate in the -2 and +1 binding subsites, PorB tolerates the presence of 3-6-anhydro-L-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The beta-agarase AgaD requires at least five consecutive agarose units (DP10) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1 and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans.,Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M J Biol Chem. 2012 Jul 9. PMID:22778272[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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