scholarly journals Function of the Family-9 and Family-22 Carbohydrate-Binding Modules in a Modular β-1,3-1,4-Glucanase/Xylanase Derived fromClostridium stercorariumXyn10B

2005 ◽  
Vol 69 (8) ◽  
pp. 1562-1567 ◽  
Author(s):  
Guangshan ZHAO ◽  
Ehsan ALI ◽  
Rie ARAKI ◽  
Makiko SAKKA ◽  
Tetsuya KIMURA ◽  
...  
Keyword(s):  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
The Family

Essential role of the family-22 carbohydrate-binding modules for β-1,3-1,4-glucanase activity of Clostridium stercorarium Xyn10B

FEBS Letters ◽  
2004 ◽  
Vol 561 (1-3) ◽  
pp. 155-158 ◽  
Author(s):  
Rie Araki ◽  
Mursheda K Ali ◽  
Makiko Sakka ◽  
Tetsuya Kimura ◽  
Kazuo Sakka ◽  
...  
Keyword(s):  
Essential Role ◽  
Carbohydrate Binding ◽  
Glucanase Activity ◽  
Carbohydrate Binding Modules ◽  
The Family

scholarly journals The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity

Glycobiology ◽  
2009 ◽  
Vol 19 (6) ◽  
pp. 615-623 ◽  
Author(s):  
Gurvan Michel ◽  
Tristan Barbeyron ◽  
Bernard Kloareg ◽  
Mirjam Czjzek
Keyword(s):  
Substrate Specificity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
The Family

scholarly journals Overproduction, purification, crystallization and preliminary X-ray characterization of the family 46 carbohydrate-binding module (CBM46) of endo-β-1,4-glucanase B (CelB) fromBacillus halodurans

2014 ◽  
Vol 70 (6) ◽  
pp. 754-757 ◽  
Author(s):  
Immacolata Venditto ◽  
Helena Santos ◽  
Luís M. A. Ferreira ◽  
Kazuo Sakka ◽  
Carlos M. G. A. Fontes ◽  
...  
Keyword(s):  
Metal Ion ◽  
Plant Cell Wall ◽  
Bacillus Halodurans ◽  
Carbohydrate Binding ◽  
Cell Wall Polysaccharides ◽  
Native Form ◽  
Carbohydrate Binding Modules ◽  
The Family ◽  
Carbon Recycling

Plant cell-wall polysaccharides offer an abundant energy source utilized by many microorganisms, thus playing a central role in carbon recycling. Aerobic microorganisms secrete carbohydrate-active enzymes (CAZymes) that catabolize this composite structure, comprising cellulose, hemicellulose and lignin, into simple compounds such as glucose. Carbohydrate-binding modules (CBMs) enhance the efficacy of associated CAZYmes. They are organized into families based on primary-sequence homology. CBM family 46 contains more than 40 different members, but has yet to be fully characterized. Here, a recombinant derivative of the C-terminal family 46 CBM module (BhCBM46) ofBacillus haloduransendo-β-1,4-glucanase B (CelB) was overexpressed inEscherichia coliand purified by immobilized metal-ion affinity chromatography. Preliminary structural characterization was carried out onBhCBM46 crystallized in different conditions. The crystals ofBhCBM46 belonged to the tetragonal space groupI4122. Data were collected for the native form and a selenomethionine derivative to 2.46 and 2.3 Å resolution, respectively. TheBhCBM46 structure was determined by a single-wavelength anomalous dispersion experiment usingAutoSolfrom thePHENIXsuite.

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.

Pectate lyase 10A from Pseudomonas cellulosa is a modular enzyme containing a family 2a carbohydrate-binding module

2001 ◽  
Vol 355 (1) ◽  
pp. 155-165 ◽  
Author(s):  
Ian E. BROWN ◽  
Marie H. MALLEN ◽  
Simon J. CHARNOCK ◽  
Gideon J. DAVIES ◽  
Gary W. BLACK
Keyword(s):  
Sequence Similarity ◽  
Functional Module ◽  
Pectate Lyase ◽  
Crystalline Cellulose ◽  
Carbohydrate Binding ◽  
High Sequence Identity ◽  
Pectate Lyases ◽  
Carbohydrate Binding Modules ◽  
The Family ◽  
Catalytic Module

Pectate lyase 10A (Pel10A) enzyme from Pseudomonas cellulosa is composed of 649 residues and has a molecular mass of 68.5kDa. Sequence analysis revealed that Pel10A contained a signal peptide and two serine-rich linker sequences that separate three modules. Sequence similarity was seen between the 9.2kDa N-terminal module of Pel10A and family 2a carbohydrate-binding modules (CBMs). This N-terminal module of Pel10A was shown to encode an independently functional module with affinity to crystalline cellulose. A high sequence identity of 66% was seen between the 14.2kDa central module of Pel10A and the functionally uncharacterized central modules of the xylan-degrading enzymes endoxylanase 10B, arabinofuranosidase 62C and esterase 1D, also from P. cellulosa. The 35.8kDa C-terminal module of Pel10A was shown to have 30 and 36% identities with the family 10 pectate lyases from Azospirillum irakense and an alkaliphilic strain of Bacillus sp. strain KSM-P15, respectively. This His-tagged C-terminal module of the Pel10A was shown to encode an independent catalytic module (Pel10Acm). Pel10Acm was shown to cleave pectate and pectin in an endo-fashion and to have optimal activity at pH10 and in the presence of 2mM Ca2+. Highest enzyme activity was detected at 62°C. Pel10Acm was shown to be most active against pectate (i.e. polygalacturonic acid) with progressively less activity against 31, 67 and 89% esterified citrus pectins. These data suggest that Pel10A has a preference for sequences of non-esterified galacturonic acid residues. Significantly, Pel10A and the P. cellulosa rhamnogalacturonan lyase 11A, in the accompanying article [McKie, Vincken, Voragen, van den Broek, Stimson and Gilbert (2001) Biochem. J. 355, 167–177], are the first CBM-containing pectinases described to date.

scholarly journals Molecular Basis for the Selectivity and Specificity of Ligand Recognition by the Family 16 Carbohydrate-binding Modules fromThermoanaerobacterium polysaccharolyticumManA

2007 ◽  
Vol 283 (18) ◽  
pp. 12415-12425 ◽  
Author(s):  
Brian Bae ◽  
Samuel Ohene-Adjei ◽  
Svetlana Kocherginskaya ◽  
Roderick I. Mackie ◽  
M. Ashley Spies ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Ligand Recognition ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
The Family

scholarly journals The interaction of carbohydrate-binding modules with insoluble non-crystalline cellulose is enthalpically driven

2005 ◽  
Vol 385 (2) ◽  
pp. 479-484 ◽  
Author(s):  
Alisdair B. BORASTON
Keyword(s):  
Configurational Entropy ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Titration Calorimetry ◽  
Bacillus Species ◽  
Crystalline Cellulose ◽  
Regenerated Cellulose ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules ◽  
The Family

Natural cellulose exists as a composite of cellulose forms, which can be broadly characterized as crystalline or non-crystalline. The recognition of both of these forms of cellulose by the CBMs (carbohydrate-binding modules) of microbial glycoside hydrolases is important for the efficient natural and biotechnological conversion of cellulosic biomass. The category of CBM that binds insoluble non-crystalline cellulose does so with an affinity approx. 10–20-fold greater than their affinity for cello-oligosaccharides and/or soluble polysaccharides. This phenomenon has been assumed to originate from the effects of changes in configurational entropy upon binding. The loss of configurational entropy is thought to be less profound upon binding to conformationally restrained insoluble non-crystalline cellulose, resulting in larger free energies of binding. However, using isothermal titration calorimetry, it is shown that this is not the case for the high-affinity interactions of CcCBM17 (the family 17 CBM from EngF of Clostridium cellulovorans) and BspCBM28 (the family 28 CBM from Cel5A of Bacillus species 1139) with regenerated cellulose, an insoluble preparation of primarily non-crystalline cellulose. The enhanced free energy of binding of non-crystalline cellulose relative to cello-oligosaccharides is by virtue of improved enthalpy, not entropy.

scholarly journals Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

2021 ◽  
pp. 100638
Author(s):  
Marie Sofie Møller ◽  
Souad El Bouaballati ◽  
Bernard Henrissat ◽  
Birte Svensson
Keyword(s):  
Functional Diversity ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Modules

scholarly journals Functionalization of Cellulose-Based Hydrogels with Bi-Functional Fusion Proteins Containing Carbohydrate-Binding Modules

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3175
Author(s):  
Mariana Barbosa ◽  
Hélvio Simões ◽  
Duarte Miguel F. Prazeres
Keyword(s):  
Fusion Proteins ◽  
Fluorescent Protein ◽  
Protein A ◽  
Chemical Properties ◽  
Main Idea ◽  
Bioactive Molecules ◽  
Scaffolding Protein ◽  
Carbohydrate Binding ◽  
Biological Interactions ◽  
Carbohydrate Binding Modules

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

scholarly journals Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Hsing Liu ◽  
Yu-Chen Lin ◽  
Chen-Shuan Chung ◽  
Kevin Liu ◽  
Ya-Hui Chang ◽  
...  
Keyword(s):  
Markov Models ◽  
Protein Domains ◽  
Degradation Pathway ◽  
The Other ◽  
Carbohydrate Binding ◽  
Gram Stain ◽  
Active Protein ◽  
Metabolic Potential ◽  
Independent Validation ◽  
Carbohydrate Binding Modules

AbstractBowel microbiota is a “metaorgan” of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the “other glycan degradation” pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = −0.97, p < 0.002) between the scores and the abundance of “glycogen degradation” in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10−4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10−5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.

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