scholarly journals A classification of glycosyl hydrolases based on amino acid sequence similarities

1991 ◽  
Vol 280 (2) ◽  
pp. 309-316 ◽  
Author(s):  
B Henrissat
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mechanism Of Action ◽  
Classification System ◽  
Structural Data ◽  
Amino Acid Sequences ◽  
Steady Increase ◽  
Glycosyl Hydrolases ◽  
Sequence Similarities

The amino acid sequences of 301 glycosyl hydrolases and related enzymes have been compared. A total of 291 sequences corresponding to 39 EC entries could be classified into 35 families. Only ten sequences (less than 5% of the sample) could not be assigned to any family. With the sequences available for this analysis, 18 families were found to be monospecific (containing only one EC number) and 17 were found to be polyspecific (containing at least two EC numbers). Implications on the folding characteristics and mechanism of action of these enzymes and on the evolution of carbohydrate metabolism are discussed. With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised.

scholarly journals New families in the classification of glycosyl hydrolases based on amino acid sequence similarities

1993 ◽  
Vol 293 (3) ◽  
pp. 781-788 ◽  
Author(s):  
B Henrissat ◽  
A Bairoch
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Sequence ◽  
Sequence Data ◽  
Data Bank ◽  
The Other ◽  
Glycosyl Hydrolases ◽  
Protein Sequence Data ◽  
Sequence Similarities

301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis of amino-acid-sequence similarities [Henrissat (1991) Biochem. J. 280, 309-316]. Approximately half of the families were found to be monospecific (containing only one EC number), whereas the other half were found to be polyspecific (containing at least two EC numbers). A > 60% increase in sequence data for glycosyl hydrolases (181 additional enzymes or enzyme domains sequences have since become available) allowed us to update the classification not only by the addition of more members to already identified families, but also by the finding of ten new families. On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank.

scholarly journals A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities

1998 ◽  
Vol 329 (3) ◽  
pp. 719-719 ◽  
Author(s):  
J. A. CAMPBELL ◽  
G. J. DAVIES ◽  
V. BULONE ◽  
B. HENRISSAT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarities

scholarly journals Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases

1996 ◽  
Vol 318 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Roberto A GEREMIA ◽  
E Alejandro PETRONI ◽  
Luis IELPI ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Hydrophobic Cluster Analysis ◽  
Alignment Algorithms ◽  
Automatic Alignment ◽  
Genes Encoding ◽  
Sequence Similarities

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].

scholarly journals Classification of glycosyl hydrolases based on structural homology

2015 ◽  
Vol 2 (1) ◽  
pp. 1-9
Author(s):  
László Fülöp ◽  
Tamás Ponyi
Keyword(s):  
Amino Acid ◽  
Classification System ◽  
Catalytic Domain ◽  
Graphical Representation ◽  
Glycosyl Hydrolase ◽  
Evolutionary Relationship ◽  
Structural Similarity ◽  
Glycosyl Hydrolases ◽  
Automated Method

Glycosyl hydrolases are a well-known group of enzymes, which hydrolyze the glycosidic bond between carbohydrates, or between a carbohydrate and different molecules. Glycosyl hydrolases play a vital role in the human body, and are widely used in industrial applications. Glycosyl hydrolases classification is based on substrate specificity and amino acid or nucleotide sequence similarity which reflects their evolutionary relationship. Our aim, in this study, was to carry out the classification of glycosyl hydrolases, based solely on structural similarity which was made possible by the several structures available in the databases and the availability of computing power to conduct such a computationally intensive task, in a reasonable time-frame. It was also aimed that the structural similarity based classification be compared to the present classification system. Based on an all-against-all comparison, we conducted a structural comparison of glycosyl hydrolases. The results are presented graphically. The graphical representation defined 24 structurally homologous classes. The classification was validated using Cα - Cα distance analysis and amino acid sequence cluster analysis. Advantages of this method are that – being an automated method – it is fast, simple and reproducible. Glycosyl hydrolases could be classified into 24 separate classes. N-glycosyl and O-glycosyl hydrolases (both forming binding and catalytic domain classes as well) were clearly different, the former consisting of 8 classes, and the latter consisting of 16 classes. Structural classes simplified the previous classification system. This classification represents the current glycosyl hydrolase family system, but also extends it especially concerning the clan system.

scholarly journals A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities

1997 ◽  
Vol 326 (3) ◽  
pp. 929-939 ◽  
Author(s):  
James A. CAMPBELL ◽  
Gideon J. DAVIES ◽  
Vincent BULONE ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarities

scholarly journals Genetic and Biochemical Characterization of a Highly Thermostable α-l-Arabinofuranosidase fromThermobacillus xylanilyticus

2000 ◽  
Vol 66 (4) ◽  
pp. 1734-1736 ◽  
Author(s):  
Takoua Debeche ◽  
Nicola Cummings ◽  
Ian Connerton ◽  
Philippe Debeire ◽  
Michael J. O'Donohue
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Classification System ◽  
Biochemical Characterization ◽  
Glycosyl Hydrolase ◽  
Gene Encoding ◽  
Ph Range ◽  
Sequence Similarities

ABSTRACT The gene encoding an α-l-arabinofuranosidase fromThermobacillus xylanilyticus D3, AbfD3, was isolated. Characterization of the purified recombinant α-l-arabinofuranosidase produced in Escherichia coli revealed that it is highly stable with respect to both temperature (up to 90°C) and pH (stable in the pH range 4 to 12). On the basis of amino acid sequence similarities, this 56,071-Da enzyme could be assigned to family 51 of the glycosyl hydrolase classification system. However, substrate specificity analysis revealed that AbfD3, unlike the majority of F51 members, displays high activity in the presence of polysaccharides.

The minimal amino acid sequence of the insulin-potentiating fragments of human growth hormone: its mechanism of action

Diabetes ◽  
1980 ◽  
Vol 29 (10) ◽  
pp. 782-787 ◽  
Author(s):  
F. M. Ng ◽  
J. Bornstein ◽  
C. E. Pullin ◽  
J. O. Bromley ◽  
S. L. Macaulay
Keyword(s):  
Growth Hormone ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Human Growth Hormone ◽  
Mechanism Of Action ◽  
Human Growth

scholarly journals The amino acid sequence of cytochromes c-551 from three species of Pseudomonas

1973 ◽  
Vol 131 (3) ◽  
pp. 485-498 ◽  
Author(s):  
R. P. Ambler ◽  
Margaret Wynn
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Cytochrome C ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Mitochondrial Cytochrome ◽  
Cytochromes C ◽  
Lending Library ◽  
Single Peptide

The amino acid sequences of the cytochromes c-551 from three species of Pseudomonas have been determined. Each resembles the protein from Pseudomonas strain P6009 (now known to be Pseudomonas aeruginosa, not Pseudomonas fluorescens) in containing 82 amino acids in a single peptide chain, with a haem group covalently attached to cysteine residues 12 and 15. In all four sequences 43 residues are identical. Although by bacteriological criteria the organisms are closely related, the differences between pairs of sequences range from 22% to 39%. These values should be compared with the differences in the sequence of mitochondrial cytochrome c between mammals and amphibians (about 18%) or between mammals and insects (about 33%). Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50015 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.

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