Abstract
AlyQ from Persicobacter sp. CCB-QB2 is an alginate lyase with three domains — a carbohydrate-binding domain modestly resembling family 16 carbohydrate-binding module (CBM16), a family 32 CBM (CBM32) domain, and an alginate lyase domain belonging to polysaccharide lyase family 7 (PL7). Although AlyQ can also act on polyguluronate (poly-G) and polymannuronate (poly-M), it is most active on alginate. Studies with truncated AlyQ showed that the CBM32 domain did not contribute to enhancing AlyQ’s activity under the assayed conditions. Nevertheless, it could bind to cleaved but not intact alginate, indicating that the CBM32 domain recognises alginate termini. The crystal structure containing both CBM32 and catalytic domains show that they 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, meanwhile, shares a conserved substrate-binding groove, and the presence of two negatively charged Asp residues may dictate substrate specificity especially at subsite +1. As Persicobacter sp. CCB-QB2 was unable to utilise alginate, AlyQ may function to help the bacterium degrade cell walls more efficiently.
Highlights
Alginate is a major component in the cell walls of brown algae, composed of mannuronate (M) and guluronate (G) arranged as 1,4-linked polysaccharides
CCB-QB2, an agarolytic bacterium isolated from seaweed in a coastal area of Malaysia[9], was found to encode a polysaccharide lyase family 7 (PL7) alginate lyase, AlyQ, in its genome
AlyQ’s first domain moderately resembles family 16 carbohydrate-binding modules (CBMs) (CBM16), while the second domain belongs to family 32 CBM (CBM32)
Summary
Alginate is a major component in the cell walls of brown algae, composed of mannuronate (M) and guluronate (G) arranged as 1,4-linked polysaccharides It is commercially extracted from seaweed and widely used in the food and pharmaceutical industries. Among the presently classified 23 polysaccharide lyase (PL) families in the CAZy (Carbohydrate Active enZyme) database (http://www.cazy.org/), alginate lyases are found in families PL5, PL6, PL7, PL14, PL15, PL17 and PL18. These families are structurally diverse, with PL7, PL14 and PL18 alginate lyases, for example, sharing a β-jelly roll topology[6]. Like many multidomain alginate lyases, AlyQ contains two additional carbohydrate-binding modules (CBMs) at its N terminus. In order to understand the relationship between these CBMs and the catalytic domain, we have characterized AlyQ’s activity and substrate binding, as well as solved the structure of a truncated version containing the CBM32 and catalytic domains
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