scholarly journals Recognition of the Helical Structure of β-1,4-Galactan by a New Family of Carbohydrate-binding Modules

2010 ◽  
Vol 285 (46) ◽  
pp. 35999-36009 ◽  
Author(s):  
Melissa Cid ◽  
Henriette Lodberg Pedersen ◽  
Satoshi Kaneko ◽  
Pedro M. Coutinho ◽  
Bernard Henrissat ◽  
...  
Keyword(s):  
Helical Structure ◽  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

scholarly journals A Tomato Endo-β-1,4-glucanase, SlCel9C1, Represents a Distinct Subclass with a New Family of Carbohydrate Binding Modules (CBM49)

2007 ◽  
Vol 282 (16) ◽  
pp. 12066-12074 ◽  
Author(s):  
Breeanna R. Urbanowicz ◽  
Carmen Catalá ◽  
Diana Irwin ◽  
David B. Wilson ◽  
Daniel R. Ripoll ◽  
...  
Keyword(s):  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

α-Glucan Recognition by a New Family of Carbohydrate-Binding Modules Found Primarily in Bacterial Pathogens†

Biochemistry ◽  
2004 ◽  
Vol 43 (49) ◽  
pp. 15633-15642 ◽  
Author(s):  
Alicia Lammerts van Bueren ◽  
Ron Finn ◽  
Juan Ausió ◽  
Alisdair B. Boraston
Keyword(s):  
Bacterial Pathogens ◽  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

scholarly journals Divergent Modes of Glycan Recognition by a New Family of Carbohydrate-binding Modules

2008 ◽  
Vol 283 (18) ◽  
pp. 12604-12613 ◽  
Author(s):  
Katie J. Gregg ◽  
Ron Finn ◽  
D. Wade Abbott ◽  
Alisdair B. Boraston
Keyword(s):  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose

2001 ◽  
Vol 355 (1) ◽  
pp. 167-177 ◽  
Author(s):  
Vincent A. MCKIE ◽  
Jean-Paul VINCKEN ◽  
Alphons G. J. VORAGEN ◽  
Lambertus A. M. VAN DEN BROEK ◽  
Elaine STIMSON ◽  
...  
Keyword(s):  
Main Chain ◽  
Catalytic Domain ◽  
Modular Structure ◽  
Carbohydrate Binding ◽  
Aerobic Bacterium ◽  
Modular Architecture ◽  
Recombinant Phage ◽  
Terminal Domain ◽  
New Family ◽  
Carbohydrate Binding Modules

Pseudomonas cellulosa is an aerobic bacterium that synthesizes an extensive array of modular cellulases and hemicellulases, which have a modular architecture consisting of catalytic domains and distinct non-catalytic carbohydrate-binding modules (CBMs). To investigate whether the main-chain-cleaving pectinases from this bacterium also have a modular structure, a library of P. cellulosa genomic DNA, constructed in λZAPII, was screened for pectinase-encoding sequences. A recombinant phage that attacked arabinan, galactan and rhamnogalacturonan was isolated. The encoded enzyme, designated Rgl11A, had a modular structure comprising an N-terminal domain that exhibited homology to Bacillus and Streptomyces proteins of unknown function, a middle domain that exhibited sequence identity to fibronectin-3 domains, and a C-terminal domain that was homologous to family 2a CBMs. Expression of the three modules of the Pseudomonas protein in Escherichia coli showed that its C-terminal module was a functional cellulose-binding domain, and the N-terminal module consisted of a catalytic domain that hydrolysed rhamnogalacturonan-containing substrates. The activity of Rgl11A against apple- and potato-derived rhamnogalacturonan substrates indicated that the enzyme had a strong preference for rhamnogalacturonans that contained galactose side chains, and which were not esterified. The enzyme had an absolute requirement for calcium, a high optimum pH, and catalysis was associated with an increase in absorbance at 235nm, indicating that glycosidic bond cleavage was mediated via a β-elimination mechanism. These data indicate that Rgl11A is a rhamnogalacturonan lyase and, together with the homologous Bacillus and Streptomyces proteins, comprise a new family of polysaccharide lyases. The presence of a family 2a CBM in Rgl11A, and in a P. cellulosa pectate lyase described in the accompanying paper [Brown, Mallen, Charnock, Davies and Black (2001) Biochem. J. 355, 155–165] suggests that the capacity to bind cellulose plays an important role in the activity of main-chain-cleaving Pseudomonas pectinases, in addition to cellulases and hemicellulases.

scholarly journals Characterization of a galactosyl-binding protein module from a Cellvibrio japonicus endo-xyloglucanase defines a new family of Carbohydrate Binding Modules

2020 ◽  
pp. AEM.02634-20
Author(s):  
Mohamed A. Attia ◽  
Harry Brumer
Keyword(s):  
Binding Protein ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Substrate Affinity ◽  
Carbohydrate Binding ◽  
Carbohydrate Active Enzymes ◽  
Plant Polysaccharides ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, e.g. by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is valuable source for CAZyme and CBM discovery and characterization, due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (“X181”), and a Glycoside Hydrolase Family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase [Attia et al. 2018. Biotechnol. Biofuels, 11: 45]. In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest product of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes.Importance This study reveals Carbohydrate Binding Module Family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the Carbohydrate-Active Enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.

Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Martin Machovič ◽  
Štefan Janeček
Keyword(s):  
Binding Domain ◽  
Carbohydrate Binding ◽  
Enzyme Specificity ◽  
Conserved Sequence ◽  
Domain Evolution ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
The Family ◽  
Branching Enzymes ◽  
The Individual

AbstractGlycoside hydrolase (GH) family 13 comprises about 30 different specificities. Four of them have been proposed to form the GH13 pullulanase subfamily: pullulanase, isoamylase, maltooligosyl trehalohydrolase and branching enzyme forming the seven CAZy GH13 subfamilies: GH13 8-GH13 14. Recently, a new family of carbohydrate-binding modules (CBMs), the family CBM48 has been established containing the putative starch-binding domains from the pullulanase subfamily, the β-subunit of AMP-activated protein kinase and some other GH13 enzymes with pullulanase and/or α-amylase-pullulanase specificity. Since all of these enzymes are multidomain proteins and the structure for at least one representative of each enzyme specificity has already been determined, the main goal of the present study was to elucidate domain evolution within this GH13 pullulanase subfamily (84 real enzymes) focusing on the CBM48 module. With regard to CBM48 positioning in the amino acid sequence, the N-terminal end of a protein appears to be a predominant position. This is especially true for isoamylases and maltooligosyl trehalohydrolases. Secondary structure-based alignment of CBM modules from CBM48, CBM20 and CBM21 revealed that several residues known as consensus for CBM20 and CBM21 could also be identified in CBM48, but only branching enzymes possess the aromatic residues that correspond with the two tryptophans forming the evolutionary conserved starch-binding site 1 in CBM20. The evolutionary trees constructed for the individual domains, complete alignment, and the conserved sequence regions of the α-amylase family were found to be comparable to each other (except for the C-domain tree) with two basic parts: (i) branching enzymes and maltooligosyl trehalohydrolases; and (ii) pullulanases and isoamylases. Taxonomy was respected only within clusters with pure specificity, i.e. the evolution of CBM48 reflects the evolution of specificities rather than evolution of species. This is a feature different from the one observed for the starch-binding domain of the family CBM20 where the starch-binding domain evolution reflects the evolution of species.

scholarly journals Alpha-Agarases Define a New Family of Glycoside Hydrolases, Distinct from Beta-Agarase Families

2007 ◽  
Vol 73 (14) ◽  
pp. 4691-4694 ◽  
Author(s):  
Didier Flament ◽  
Tristan Barbeyron ◽  
Murielle Jam ◽  
Philippe Potin ◽  
Mirjam Czjzek ◽  
...  
Keyword(s):  
Gene Product ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Gene Encoding ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Type 3

ABSTRACT The gene encoding the α-agarase from “Alteromonas agarilytica” (proposed name) has been cloned and sequenced. The gene product (154 kDa) is unrelated to β-agarases and instead belongs to a new family of glycoside hydrolases (GH96). The α-agarase also displays a complex modularity, with the presence of five thrombospondin type 3 repeats and three carbohydrate-binding modules.

scholarly journals X4 Modules Represent a New Family of Carbohydrate-binding Modules That Display Novel Properties

2004 ◽  
Vol 279 (22) ◽  
pp. 22953-22963 ◽  
Author(s):  
David N. Bolam ◽  
Hefang Xie ◽  
Gavin Pell ◽  
Deborah Hogg ◽  
Greta Galbraith ◽  
...  
Keyword(s):  
Carbohydrate Binding ◽  
New Family ◽  
Carbohydrate Binding Modules

Identification of novel β-mannan- and β-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules

2001 ◽  
Vol 356 (3) ◽  
pp. 791-798 ◽  
Author(s):  
Anwar SUNNA ◽  
Moreland D. GIBBS ◽  
Peter L. BERGQUIST
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Experimental Characterization ◽  
Carbohydrate Polymers ◽  
New Family ◽  
Carbohydrate Binding Modules ◽  
Long Chain

Many glycoside hydrolases, which degrade long-chain carbohydrate polymers, possess distinct catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). On the basis of conserved protein secondary structure, we describe here the identification and experimental characterization of novel type of mannanase-associated mannan-binding module and also characterization of two CBM family 4 laminarinase-associated β-glucan-binding modules. These modules are predicted to belong to a superfamily of CBMs which include families 4, 16, 17, 22 and a proposed new family, family 27.

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