Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold

2013 ◽  
Vol 77 (7) ◽  
pp. 1363-1371 ◽  
Author(s):  
Zui FUJIMOTO
Keyword(s):  
Structure And Function ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
And Function

scholarly journals The carbohydrate-binding module family 20 - diversity, structure, and function

FEBS Journal ◽  
2009 ◽  
Vol 276 (18) ◽  
pp. 5006-5029 ◽  
Author(s):  
Camilla Christiansen ◽  
Maher Abou Hachem ◽  
Štefan Janeček ◽  
Anders Viksø-Nielsen ◽  
Andreas Blennow ◽  
...  
Keyword(s):  
Structure And Function ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
And Function ◽  
Diversity Structure

scholarly journals Structure and function of accessory Sec proteins involved in the adhesin export pathway of Streptococcus gordonii

2017 ◽  
Author(s):  
Yu Chen ◽  
Barbara A. Bensing ◽  
Ravin Seepersaud ◽  
Wei Mi ◽  
Maofu Liao ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Pathogenic Bacteria ◽  
Structure And Function ◽  
Host Cells ◽  
Carbohydrate Binding ◽  
Streptococcus Gordonii ◽  
Carbohydrate Binding Proteins ◽  
Sec Proteins ◽  
And Function ◽  
Complex Crystal

ABSTRACTMany pathogenic bacteria, including Streptococcus gordonii, possess a pathway for the export of a single serine-rich-repeat protein that mediates the adhesion of bacteria to host cells and the extracellular matrix. These adhesins are O-glycosylated by several cytosolic glycosyltransferases and require three accessory Sec proteins (Asp1-3) for export, but how the adhesins are processed for secretion is not well defined. Here, we show that O-glycosylation of S. gordonii adhesin GspB occurs in a sequential manner by three enzymes (GtfA/B, Nss, Gly) that attach N-acetylglucosamine and glucose to Ser/Thr residues. The modified substrate is subsequently transferred from the last glycosyltransferase to the Asp1/2/3 complex. Crystal structures show that both Asp1 and Asp3 are related to carbohydrate binding proteins. Asp1 also has an affinity for phospholipids, which is attenuated by Asp2. These results suggest a mechanism for the modification of adhesin in the cytosol and its subsequent targeting to the export machinery.

scholarly journals The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases

2011 ◽  
Vol 286 (17) ◽  
pp. 15483-15495 ◽  
Author(s):  
Alan Cartmell ◽  
Lauren S. McKee ◽  
Maria J. Peña ◽  
Johan Larsbrink ◽  
Harry Brumer ◽  
...  
Keyword(s):  
Structure And Function ◽  
Glycoside Hydrolases ◽  
And Function

scholarly journals Domain Analysis of a Modular α-l-Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium Fibrobacter succinogenes S85

2010 ◽  
Vol 192 (20) ◽  
pp. 5424-5436 ◽  
Author(s):  
Shosuke Yoshida ◽  
Charles W. Hespen ◽  
Robert L. Beverly ◽  
Roderick I. Mackie ◽  
Isaac K. O. Cann
Keyword(s):  
Plant Cell Wall ◽  
Catalytic Efficiency ◽  
Glycoside Hydrolases ◽  
Site Directed Mutagenesis ◽  
Biofuel Production ◽  
Carbohydrate Binding ◽  
Fibrobacter Succinogenes ◽  
Carbohydrate Binding Module ◽  
Degrading Bacterium ◽  
Catalytic Module

ABSTRACT Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from Fibrobacter succinogenes S85. The recombinant protein showed α-l-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The F. succinogenes AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique β-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and F. succinogenes-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher k cat for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the Km for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.

scholarly journals Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

2020 ◽  
Author(s):  
Japheth E. Gado ◽  
Brent E. Harrison ◽  
Mats Sandgren ◽  
Jerry Ståhlberg ◽  
Gregg T. Beckham ◽  
...  
Keyword(s):  
Machine Learning ◽  
Active Site ◽  
Catalytic Domain ◽  
Cellulose Degradation ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Functional Variation ◽  
Functional Relationships ◽  
Experimental Findings ◽  
And Function

AbstractFamily 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, comprised of a catalytic domain attached to a carbohydrate binding module (CBM) via a flexible linker, and exhibit a long active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical biological and industrial importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, using the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy. The lengths of the A4, B2, B3, and B4 loops were strongly correlated with functional subtype across the GH7 family. Position-specific classification rules were derived such that specific amino acids at 42 different sequence positions predicted the functional subtype with accuracies greater than 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. We propose these positions play vital roles in the functional variation of GH7 cellulases. Taken together, our results complement numerous experimental findings and present functional relationships that can be applied when prospecting GH7 cellulases from nature, for sequence annotation, and to understand or manipulate function.

scholarly journals Structure and Function of Family 50 Carbohydrate Binding Modules (LysM Domains) from Pteris ryukyuensis Chitinase-A

2009 ◽  
Vol 56 (2) ◽  
pp. 97-104
Author(s):  
Takayuki Ohnuma ◽  
Shoko Onaga ◽  
Katsuyoshi Murata ◽  
Tamo Fukamizo ◽  
Toki Taira ◽  
...  
Keyword(s):  
Structure And Function ◽  
Carbohydrate Binding ◽  
Chitinase A ◽  
Carbohydrate Binding Modules ◽  
And Function

scholarly journals A mannanase, ManA, of the polycentric anaerobic fungusOrpinomycessp. strain PC-2 has carbohydrate binding and docking modules

2005 ◽  
Vol 51 (7) ◽  
pp. 559-568 ◽  
Author(s):  
Eduardo A Ximenes ◽  
Huizhong Chen ◽  
Irina A Kataeva ◽  
Michael A Cotta ◽  
Carlos R Felix ◽  
...  
Keyword(s):  
Specific Activity ◽  
High Specific Activity ◽  
Glycoside Hydrolases ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
Amino Acid Residues ◽  
Anaerobic Fungus ◽  
Ph Profile ◽  
Catalytic Module ◽  
Cellulose Binding

The anaerobic fungus Orpinomyces sp. strain PC-2 produces a broad spectrum of glycoside hydrolases, most of which are components of a high molecular mass cellulosomal complex. Here we report about a cDNA (manA) having 1924 bp isolated from the fungus and found to encode a polypeptide of 579 amino acid residues. Analysis of the deduced sequence revealed that it had a mannanase catalytic module, a family 1 carbohydrate-binding module, and a noncatalytic docking module. The catalytic module was homologous to aerobic fungal mannanases belonging to family 5 glycoside hydrolases, but unrelated to the previously isolated mannanases (family 26) of the anaerobic fungus Piromyces. No mannanase activity could be detected in Escherichia coli harboring a manA-containing plasmid. The manA was expressed in Saccharomyces cerevisiae and ManA was secreted into the culture medium in multiple forms. The purified extracellular heterologous mannanase hydrolyzed several types of mannan but lacked activity against cellulose, chitin, or β-glucan. The enzyme had high specific activity toward locust bean mannan and an extremely broad pH profile. It was stable for several hours at 50 °C, but was rapidly inactivated at 60 °C. The carbohydrate-binding module of the Man A produced separately in E. coli bound preferably to insoluble lignocellulosic substrates, suggesting that it might play an important role in the complex enzyme system of the fungus for lignocellulose degradation.Key words: Orpinomyces, anaerobic fungi, mannanase, cellulose-binding module, cellulosome.

scholarly journals Site-directed Mutagenesis of a β-Glycoside Hydrolase fromLentinula edodes

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 59 ◽  
Author(s):  
Jing-Jing Chen ◽  
Xiao Liang ◽  
Tian-Jiao Chen ◽  
Jin-Ling Yang ◽  
Ping Zhu
Keyword(s):  
Glycoside Hydrolase ◽  
Lentinula Edodes ◽  
Catalytic Efficiency ◽  
Structure And Function ◽  
Glycoside Hydrolases ◽  
Site Directed Mutagenesis ◽  
Substrate Affinity ◽  
And Function ◽  
The Relationship ◽  
Loop Conformation

The β-glycoside hydrolases (LXYL-P1−1 and LXYL-P1−2) from Lentinula edodes (strain M95.33) can specifically hydrolyze 7-β-xylosyl-10-deacetyltaxol (XDT) to form 10-deacetyltaxol for the semi-synthesis of Taxol. Our previous study showed that both the I368T mutation in LXYL-P1−1 and the T368E mutation in LXYL-P1−2 could increase the enzyme activity, which prompted us to investigate the effect of the I368E mutation on LXYL-P1−1 activity. In this study, the β-xylosidase and β-glucosidase activities of LXYL-P1−1I368E were 1.5 and 2.2 times higher than those of LXYL-P1−1. Most importantly, combination of I368E and V91S exerted the cumulative effects on the improvement of the enzyme activities and catalytic efficiency. The β-xylosidase and β-glucosidase activities of the double mutant LXYL-P1−1V91S/I368E were 3.2 and 1.7-fold higher than those of LXYL-P1−1I368E. Similarly, the catalytic efficiency of LXYL-P1−1V91S/I368E on 7-β-xylosyl-10-deacetyltaxol was 1.8-fold higher than that of LXYL-P1−1I368E due to the dramatic increase in the substrate affinity. Molecular docking results suggest that the V91S and I368E mutation might positively promote the interaction between enzyme and substrate through altering the loop conformation near XDT and increasing the hydrogen bonds among Ser91, Trp301, and XDT. This study lays the foundation for exploring the relationship between the structure and function of the β-glycoside hydrolases.

Development of inhibitors as research tools for carbohydrate-processing enzymes

2012 ◽  
Vol 40 (5) ◽  
pp. 913-928 ◽  
Author(s):  
Tracey M. Gloster
Keyword(s):  
Present Article ◽  
Enzyme Inhibitors ◽  
Structure And Function ◽  
Glycoside Hydrolases ◽  
Processing Enzymes ◽  
Cellular Processes ◽  
Domains Of Life ◽  
And Function ◽  
Complex Glycan ◽  
Synthesis And Degradation

Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.

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