Carbohydrate Binding Module Family 83

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• Author: Darrell Cockburn
• Responsible Curator: Nicole Koropatkin

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CAZy DB link

http://www.cazy.org/CBM83.html

Ligand specificities

Figure 1. Domain architecture of E. rectale Amy13K The CBM and GH families are indicated. The 'S' is the signal sequence and the 'anchor' is a cell wall anchoring motif. The CBM83 domain is bolded. The 'unknown' domain has no known function, however, its deletion eliminates all activity of the enzyme [1]

The founding member and first to be characterized of this family is the fifth CBM found in the cell-wall anchored GH13 enzyme Amy13K from Eubacterium rectale (Fig1). It was found to bind beta-cyclodextrin and glycogen with similar affinity, with slightly weaker affinity for maltoheptaose as determined by isothermal titration calorimetry. The module was also found to bind to corn starch granules, both from a wild-type source and from a high amylose source (HiMaize 260) with approximately equal affinity but did not demonstrate binding to potato starch or a chemically crosslinked starch (Fibersym) as determined via depletion assays. Little if any binding to amylopectin and pullulan was found when tested via affinity electrophoresis. [1].

Structural Features

Secondary structure analysis and alignments suggest they are likely to be beta-sandwich type folds similar to the CBM41 family [1].

Functionalities

This family has been found to be exclusively associated with GH13 family amylases from a quite narrow taxonomic range within Roseburia and Eubacterium rectale [1]. Removal of the only CBM83 from the E. rectale Amy13K enzyme had little effect on its activity towards amylopectin and potato starch, but resulted in a 2-fold decrease in the activity towards corn starch granules, suggesting an important role in activity towards this substrate [1]

Family Firsts

First Identified

In Roseburia inulinivorans as a predicted CBM [2]

First Characterized

From E. rectale Amy13K, establishing the family [1]

References

1. Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, and Koropatkin NM. (2018). Novel carbohydrate binding modules in the surface anchored α-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut. Mol Microbiol. 2018;107(2):249-264. DOI:10.1111/mmi.13881 |
2. Ramsay AG, Scott KP, Martin JC, Rincon MT, and Flint HJ. (2006). Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology (Reading). 2006;152(Pt 11):3281-3290. DOI:10.1099/mic.0.29233-0 |