Advances in molecular engineering of carbohydrate-binding modules

Abstract

Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.

Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains

“…Most of carbohydrate-active enzymes are modular proteins possessing, in addition to their catalytic domain, also some extra modules (Lombard et al 2014 ). Of these, the best known non-catalytic modules may be represented by CBMs (Boraston et al 2004 ; Armenta et al 2017 ). Since the family GH126 could be another α-amylase family in the system of CAZy classification (Janecek et al 2014 ; Kerenyiova and Janecek 2020 ), it could be reasonable to look for the presence of some kind of SBDs that have been currently classified in 15 different CBM families in CAZy (Janecek et al 2019 ).…”

“…The colour code for the selected residues: W, yellow; F, Y-blue; V, L, I-green; D, E-red; R, K-cyan; H-brown; Cmagenta; G, P-black ◂ Most of carbohydrate-active enzymes are modular proteins possessing, in addition to their catalytic domain, also some extra modules (Lombard et al 2014). Of these, the best known non-catalytic modules may be represented by CBMs (Boraston et al 2004;Armenta et al 2017). Since the family GH126 could be another α-amylase family in the system of CAZy classification (Janecek et al 2014; Kerenyiova and Janecek 2020), it could be reasonable to look for Fig.…”

Molecular Modelling of a Thermostable Glycoside Hydrolase from <i>Caldivirga </i><i>m</i><i>aquilingensis</i> and Its Substrate Docking Mechanism for Galactooligosaccharides Synthesis

“…It is worth noting that other residues like, alanine (Ala 266), asparagine (Asp267), serine (Ser268), Glutamic acid (Glu432), tryptophan (Trp433) and glutamine (Gln19) found surrounding the catalytic site are within hydrogen bonding distances with the glycone and aglycone playing essential roles in ligand binding and recognition of the lactose molecules and in selecting different acceptor molecules during transgalactosylation unique to this enzyme. In fact the hydroxyl, polar and aromatic side chains found in some of these residues have been reported to provide flexibility and fine-tuning of the position of the nucleophile and also stabilizing the deprotonated state of the substrate-enzyme intermediate which is beneficial for both transgalactosylation and hydrolysis [20,26]. Therefore, the orientation and establishment of bonds between the substrate and both aromatic and polar amino acids define the relevant enzymatic features, such as the affinity, specificity, and activity.…”

CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities

“…As of today, CAZy database hosts 83 CBM families, out of which cellulose-binding modules are distributed in 25 CBM families. CBMs can be majorly classified into three types: A-type (CBMs bind to surfaces of crystalline polysaccharides, e.g., cellulose, chitin), B-type (CBMs bind to internal longer sugar chains with more than four monosaccharide units) and C-type (CBMs bind to the ends of shorter sugar chains with not more than 3 monosaccharide units) (Armenta et al 2017;Boraston et al 2004;Gilbert et al 2013). The "Enzymatic activities exhibited by CBM domains" webpage can be used for finding the carbohydrate-binding modules associated with a specific enzyme module.…”