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 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 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 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].

Glycine cleavage enzyme complex: Rabbit H-protein cDNA sequence analysis and comparison to human, cow, and chicken

2000 ◽  
Vol 78 (6) ◽  
pp. 725-730 ◽  
Author(s):  
Francis Choy ◽  
Lisa Sharp ◽  
Derek A Applegarth
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Matrix Protein ◽  
Protein Gene ◽  
Mitochondrial Targeting ◽  
Reading Frame ◽  
Cleavage Enzyme ◽  
Glycine Cleavage ◽  
H Protein ◽  
Sequence Similarities

The H-protein is one of the four essential components (H-, L-, P-, and T-proteins) of the mammalian glycine cleavage enzyme complex, the major degradative pathway of glycine. We have isolated the full-length cDNA of the H-protein gene from the rabbit (Oryctolagus caniculus) by reverse transcription of liver poly-A mRNA and determined its nucleotide sequence (GenBank Acc. No. BankIt 318281 AF 231451). Similar to that in human, the rabbit H-protein gene possesses a 519-bp open reading frame that translates a 173-amino-acid (aa) protein. This reading frame is comprised of a 48-aa mitochondrial targeting sequence and a 125-aa residue that constitutes the mature mitochondrial matrix protein. In the mature protein region, there is a 95.5% nucleotide and 98.4% amino-acid sequence similarity to human. This conservation was also noted in the mature protein of the cow (Bos taurus) and chicken (Gallus domesticus), where there are a 94.1% and 85.3% nucleotide similarities, and 95.2% and 85.6% amino-acid sequence similarities, respectively. However, the targeting region is not as well conserved. Comparison of the rabbit targeting sequence to that in human, cow, and chicken reveals 84.0%, 79.2%, and 72.9% nucleotide, and 72.9%, 75.0%, and 54.2% amino-acid sequence similarities, respectively. These findings suggest that within the H-protein gene, the regions encoding the mitochondrial targeting and matrix protein may have evolved differently. Gene diversification in the former may reflect the species specificity in targeting proteins destined for the mitochondria, whereas homology in the latter suggests a very similar structure-function of the mature H-protein among these species. This homology in structure-function likely accounts for the observation that non-human H-protein can replace the human protein in the activity assay of the glycine cleavage enzyme system. This includes the biochemical diagnosis of non-ketotic hyperglycinemia (NKH) resulting from defects other than the H-protein, e.g., mutation(s) in the P-protein.Key words: glycine cleavage enzyme, H-protein, sequence comparison, non-ketotic hyperglycinemia.

scholarly journals Substrate-binding domains of glycanases from Streptomyces lividans: characterization of a new family of xylan-binding domains

1998 ◽  
Vol 330 (1) ◽  
pp. 41-45 ◽  
Author(s):  
Claude DUPONT ◽  
Martin ROBERGE ◽  
François SHARECK ◽  
Rolf MOROSOLI ◽  
Dieter KLUEPFEL
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Substrate Binding ◽  
Streptomyces Lividans ◽  
Cellulose Binding Domain ◽  
Binding Domains ◽  
New Family ◽  
Cellulose Binding ◽  
Sequence Similarities

The substrate-binding domains of six glycanases from Streptomyces lividans were investigated to determine their specificity towards cellulose and xylan. Based upon amino acid sequence similarities, four of the six domains could be assigned to existing cellulose-binding domain families. However, the binding domains of xylanase A and arabinofuranosidase B could not be classified in any of the known families and should therefore be classified as members of a new family. Evidence is also presented that this new family is one of true xylan-binding domains.

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