Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2

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.

Functional Characterization of Carbohydrate-Binding Modules in a New Alginate Lyase, TsAly7B, from Thalassomonas sp. LD5

“…The presence of CBM32 domain in AlyQ from Persicobacter sp. CCB-QB2 also did not significantly increase its activity [17]. In this study, we observed that the specific enzymatic activities of TM1 (CBM32-PL7) and TM2 (CBM9-PL7) were 4.6-fold and 6.6-fold higher than that of TM3 (the PL7 catalytic module only), respectively.…”

“…Several thousand alginate lyases have been classified into the PL5, 6,7,14,15,17,18,32,34, 36 and 39 families in the CAZy database (http://www.cazy.org/) [4,12]. Some alginate lyases are known to contain one or more carbohydrate-binding modules (CBMs); CBM13, CBM16, and CBM32 are the most common [13].…”

“…In the degradation of cellulosic substrates, CBMs have been shown to work synergistically and to produce cumulative effects [16]. In alginate lyase, CBM32s have been elucidated to participate in the recognition of alginate and impact the composition of final degradation products, which provided potential and valuable application and aroused wide interests in function of CBM [17,18]. However, the precise function of CBM9 in alginate lyases has yet to be elucidated.…”

Alginate Oligosaccharides: Production, Biological Activities, and Potential Applications

“…A1 (PDB code 2CWS; Yamasaki, Ogura, Hashimoto, Mikami, & Murata, ), AlyQ from Persicobacter sp. CCB‐QB2 (PDB code 5XNR; Sim, Furusawa, & Teh, ), and FlAlyA from Flavobacterium sp. UMI‐01 (PDB code 5Y33; Qin et al., )—hold the β‐jelly roll fold.…”

The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39

“…This type of architecture is common for many PL family enzymes, but it is less common for alginate lyases, although, in some, but not all enzymes belonging to the PL7 family, accessory modules belonging to CBM13, CBM16 and CBM32 have been identified (24)(25)(26). Currently, the precise roles of these domains in alginate lyases are poorly understood with only weak binding of the CBM32 domains to the oligosaccharide being reported (25,27).…”