4ATF

Crystal structure of inactivated mutant beta-agarase B in complex with agaro-octaose

Summary for 4ATF

• Entry DOI: 10.2210/pdb4atf/pdb
• Related: 1O4Z
• Descriptor: BETA-AGARASE B, 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose, SODIUM ION, ... (4 entities in total)
• Functional Keywords: hydrolase, polysaccharidase, agarolytic enzyme
• Biological source: ZOBELLIA GALACTANIVORANS
• Cellular location: Cell outer membrane ; Lipid-anchor : Q9RGX8
• Total number of polymer chains: 4
• Total formula weight: 148041.35

Authors

Bernard, T.,Hehemann, J.H.,Correc, G.,Jam, M.,Michel, G.,Czjzek, M. (deposition date: 2012-05-06, release date: 2012-07-25, Last modification date: 2023-12-20)

Primary citation

Hehemann, J.H.,Correc, G.,Thomas, F.,Bernard, T.,Barbeyron, T.,Jam, M.,Helbert, W.,Michel, G.,Czjzek, M.
Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine Bacterium Zobellia Galactanivorans.
J.Biol.Chem., 287:30571-, 2012

PubMed Abstract: Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although 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 β-agarase AgaD requires at least four consecutive agarose units (DP8) 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.

PubMed: 22778272
DOI: 10.1074/JBC.M112.377184

Experimental method

X-RAY DIFFRACTION (1.9 Å)