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A Bairoch

Publications and source records attributed to A Bairoch.

100 records · Page 6Linked to original sources
PubMed1989

A unique signature identifies a family of zinc-dependent metallopeptidases.

The primary sequence motif HExxH has been found in many zinc-dependent endopeptidases. We show that a larger signature comprising this sequence is common to most of the known zinc-dependent endopeptidases, and that the presence of the signature can be indicative of membership in the family. A search of the protein sequence databases for entries containing the signature retrieved several unexpected potential zinc endopeptidases.

Amino Acid Sequence↗
PubMed1989

A cross-reference table between the Protein Data Bank of macromolecular structures and the National Biomedical Research Foundation-Protein Identification Resource amino acid sequence data bank.

The National Biomedical Research Foundation-Protein Identification Resource (NBRF-PIR) and the Protein Data Bank at Brookhaven National Laboratory (PDB) both contain protein sequences. We have prepared a cross-reference index of the sequences in these data banks, and compared the data. Of the 270 cases of sequences of the same protein appearing in both data bases, for only 31% are the sequences identical. This is often the result of a difference in the state of maturation of the proteins rather than experimental error. Nevertheless is useful to be aware that the sequence information in these two data archives should not be regarded as redundant.

Amino Acid Sequence↗
PubMed1988

Using PC/GENE for protein and nucleic acid analysis.

This paper describes a series of protein analyses using the molecular biology software package PC/GENE, which runs on an IBM or compatible microcomputer. A nucleic acid sequence was first edited and then translated into an amino acid sequence. The amino acid composition, isoelectric point, molecular weight, and other properties of the sequence were determined. Programs to predict secondary structure, alpha helix membrane associations, hydrophobic and hydrophilic regions, and surface and antigenic sites from the amino acid sequence were also used. A search was made in a data base for sequences containing a region similar to a region in the protein sequence. Sequence alignments and queries of data bases can also be performed.

Amino Acid Sequence↗
PubMed1987

Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids.

TOL plasmid pWW0 and plasmid NAH7 encode catabolic enzymes required for oxidative degradation of toluene and naphthalene, respectively. The gene order of the catabolic operon of NAH7 for salicylate oxidation was determined to be: promoter--nahG (the structural gene for salicylate hydroxylase)--nahH (catechol 2.3-dioxygenase)--nahI (hydroxymuconic semialdehyde dehydrogenase)--nahN (hydroxymuconic semialdehyde hydrolase)--nahL (2-oxopent-4-enoate hydratase). This order is identical to that of the isofunctional genes of TOL plasmid pWW0. The complete nucleotide sequence of nahH was determined and compared with that of xylE, the isofunctional gene of TOL plasmid pWW0. There were 20% and 16% differences in their nucleotide and amino acid sequences, respectively. The homology between the NAH7 and TOL pWW0 plasmids ends upstream of the Shine-Dalgarno sequences of nahH and xylE, but the homology continues downstream of these genes. This observation suggested that genes for the catechol oxidative enzymes of NAH7 and TOL pWW0 were derived from a common ancestral sequence which was transferred as a discrete segment of DNA between plasmids.

Amino Acid Sequence↗
PubMed1987

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon.

The Pseudomonas putida TOL plasmid pWWO carries an operon that specifies a meta-cleavage pathway for the catabolism of benzoate and toluates whose transcription is positively regulated by the xylS gene product. Stimulation of transcription of the operon is thought to result from activation of this protein by pathway substrates/effectors. In the present study, overexpression of the xylS gene has led to identification of the regulator as a 33 kDa protein. Overexpression of xylS also resulted in partially constitutive, i.e. effector-independent expression of the meta-cleavage operon. Determination of the polynucleotide sequence of the xylS gene revealed amino acid sequence homology with several DNA binding proteins, particularly with the araC products of Escherichia coli and Salmonella typhimurium and with the nifA and ntrC products of Klebsiella pneumoniae. Homologous sequences were mainly located in an alpha-helix-turn-alpha-helix domain of the polypeptide. Interestingly, amino acid sequence homology was also found with sigma factors of E. coli (ntrA and htpR products) and Bacillus subtilis (spoIIG and phage SPOI Gp34 products) and other RNA polymerase core-interacting proteins, such as the E. coli nusA product.

Amino Acid Sequence↗
PubMedDate not supplied

Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool.

In peptide mass fingerprinting, there are frequently peptides whose masses cannot be explained. These are usually attributed to either a missed cleavage site during the chemical or enzymatic cutting process, the lack of reduction and alkylation of a protein, protein modifications like the oxidation of methionine, or the presence of protein post-translational modifications. However, they could equally be due to database errors, unusual splicing events, variants of a protein in a population, or artifactual protein modifications. Unfortunately the verification of each of these possibilities can be tedious and time-consuming. To better utilize annotated protein databases for the understanding of peptide mass fingerprinting data, we have written the program "PEPTIDEMASS". This program generates the theoretical peptide masses of any protein in the SWISS-PROT database, or of any sequence specified by the user. If the sequence is derived from the SWISS-PROT database, the program takes into account any annotations for that protein in order to generate the peptide masses. In this manner, the user can obtain the predicted masses of peptides from proteins which are known to have signal sequences, propeptides, transit peptides, simple post-translational modifications, and disulfide bonds. Users are also warned if any peptide masses are subject to change from protein isoforms, database conflicts, or an mRNA splicing variation. The program is freely accessible to the scientific community via the ExPASy World Wide Web server, at the URL address: http://www.expasy.ch/www/tools.html.

Amino Acid Sequence↗