AlyA5 belongs to the PL7 family, subfamily 5, the genome of Zobellia galactanivorans contains seven putative alginate lyase genes, five of which are localized within two clusters comprising additional carbohydrate-related genes, phylogenetic analysis. Despite a common jelly roll-fold, these striking differences of the mode of action are explained by a distinct active site topology, an open cleft in AlyA1PL7, whereas AlyA5 displays a pocket topology due to the presence of additional loops partially obstructing the catalytic groove. In contrast to PL7 alginate lyases from terrestrial bacteria, both enzymes proceed according to a calcium-dependent mechanism
the enzyme belongs to the polysaccharide lyase PL7 family. Structure and beta-elimination mechanism for glycolytic bond cleavage by Alg17c are similar to those observed for family 15 polysaccharide lyases and other lyases, evolutionary relationships and structure-based hierarchy in the classification, overview
the enzyme belongs to the polysaccharide lyase PL7 family. Structure and beta-elimination mechanism for glycolytic bond cleavage by Alg17c are similar to those observed for family 15 polysaccharide lyases and other lyases, evolutionary relationships and structure-based hierarchy in the classification, overview
AlyA5 belongs to the PL7 family, subfamily 5, the genome of Zobellia galactanivorans contains seven putative alginate lyase genes, five of which are localized within two clusters comprising additional carbohydrate-related genes, phylogenetic analysis. Despite a common jelly roll-fold, these striking differences of the mode of action are explained by a distinct active site topology, an open cleft in AlyA1PL7, whereas AlyA5 displays a pocket topology due to the presence of additional loops partially obstructing the catalytic groove. In contrast to PL7 alginate lyases from terrestrial bacteria, both enzymes proceed according to a calcium-dependent mechanism
alginate lyase dispersion of Pseudomonas aeruginosa biofilms and enzyme synergy with tobramycin are completely decoupled from catalytic activity, in vitro modeling, overview
alginate lyase dispersion of Pseudomonas aeruginosa biofilms and enzyme synergy with tobramycin are completely decoupled from catalytic activity, in vitro modeling, overview
herbivorous marine gastropods such as abalone and sea hare ingest brown algae as a major diet and degrade the dietary alginate with alginate lyase in their digestive fluid
alginate lyase consists of three domains, i.e. a carbohydrate-binding domain, a family 32 CBM domain, and an alginate lyase domain belonging to polysaccharide lyase family 7 (PL7). The CBM32 domain does not contribute to enhancing AlyQ's activity under the assayed conditions but can bind to cleaved but not intact alginate. The CBM32 and catalytic domains do not interact with one another. The CBM32 domain contains a conserved Arg that may bind to the carboxyl group of alginate. The catalytic domain shares a conserved substrate-binding groove, and the presence of two negatively charged Asp residues may dictate substrate specificity especially at subsite +1
deletion of the noncatalytic region of Aly1 causes weak changes of biochemical characteristics but increases the degradation proportions of small size-defined saturated D-mannuronate-enriched oligosaccharide substrates and unsaturated tetrasaccharide fractions without any size changes of degradable oligosaccharides
homology modeling using structure of family 7 alginate lyase from Sphingomonas sp. A1, structure-affinity relationships of aliginate lyase alyVI with its substrate, molecular docking, molecular dynamics simulations and binding free energy calculations, overview. Residues Asn138, Arg143, Asn217, and Lys308 are involved in the catalytic reaction, and van der Waals interactions are responsible for binding with the catalytic His200 and Tyr312 residues
structure-fucntion analysis, superposition of the open and closed lid loops suggests that the conformational change results in near-rigid-body motion, The open-closed movement of the lid loop decreases the accessible surface area by covering the active-site cleft., overview
homology modeling using structure of family 7 alginate lyase from Sphingomonas sp. A1, structure-affinity relationships of aliginate lyase alyVI with its substrate, molecular docking, molecular dynamics simulations and binding free energy calculations, overview. Residues Asn138, Arg143, Asn217, and Lys308 are involved in the catalytic reaction, and van der Waals interactions are responsible for binding with the catalytic His200 and Tyr312 residues