Arnaud Chatonnet

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins

The α/β-hydrolase fold is characterized by a β-sheet core of five to eight strands connected by α-helices to form a α/β/α sandwich. In most of the family members the β-strands are parallels, but some show an inversion in the order of the first strands, resulting in antiparallel orientation. The members of the superfamily diverged from a common ancestor into a number of hydrolytic enzymes with a wide range of substrate specificities, together with other proteins with no recognized catalytic activity. In the enzymes the catalytic triad residues are presented on loops, of which one, the nucleophile elbow, is the most conserved feature of the fold. Of the other proteins, which all lack from one to all of the catalytic residues, some may simply be ‘inactive’ enzymes while others are known to be involved in surface recognition functions. The ESTHER database (http://bioweb.ensam.inra.fr/esther) gathers and annotates all the published information related to gene and protein sequences of this superfamily, as well as biochemical, pharmacological and structural data, and connects them so as to provide the bases for studying structure–function relationships within the family. The most recent developments of the database, which include a section on human diseases related to members of the family, are described.

aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server.

Acetylcholinesterase belongs to a family of proteins, the alpha/beta hydrolase fold family, whose constituents evolutionarily diverged from a common ancestor and share a similar structure of a central beta sheet surrounded by alpha helices. These proteins fulfil a wide range of physiological functions (hydrolases, adhesion molecules, hormone precursors) [Krejci,E., Duval,N., Chatonnet,A., Vincens,P. and Massoulié,J. (1991) Proc. Natl. Acad. Sci. USA , 88, 6647-6651]. ESTHER (for esterases, alpha/beta hydrolase enzymes and relatives) is a database aimed at collecting in one information system, sequence data together with biological annotations and experimental biochemical results related to the structure-function analysis of the enzymes of the family. The major upgrade of the database comes from the use of a new database management system: aCHEdb which uses the ACeDB program designed by Richard Durbin and Jean Thierry-Mieg. It can be found at http://www.ensam.inra.fr/cholinesterase

The α/β fold family of proteins database and the cholinesterase gene server ESTHER

ESTHER (for esterases, alpha/betahydrolase enzyme and relatives) is a database of sequences phylogenetically related to cholinesterases. These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) sharing a similar structure of a central beta-sheet surrounded by alpha-helices. Among these proteins a wide range of functions can be found (hydrolases, adhesion molecules, hormone precursors). The purpose of ESTHER is to help comparison of structures and functions of members of the family. Since the last release, new features have been added to the server. A BLAST comparison tool allows sequence homology searches within the database sequences. New sections are available: kinetics and inhibitors of cholinesterases, fasciculin-acetylcholinesterase interaction and a gene structure review. The mutation analysis compilation has been improved with three-dimensional images. A mailing list has been created.

Enzymatic Activity and Protein Interactions in Alpha/Beta Hydrolase Fold Proteins: Moonlighting Versus Promiscuity

Genes coding for members of the alpha/beta hydrolase fold superfamily of proteins are present in all known genomes. Although there is no common and essential function performed by these proteins shared in all living organisms, this fold has been used for a number of diverse functions. The ancestry of both enzymatic and protein-protein interaction capability of this structural scaffold made it an important tinkering tool kit for protein function evolution. Recently, enzymes known since a long time have been found to have a second function in acting promiscuously on alternative substrates, or to be true moonlighting proteins acting also as transporters, receptors, chaperones… The reverse situation has been encountered for adhesion proteins shown to be enzymes. This review, while not exhaustive, surveys some of the best-known examples of multiple functions in alpha/beta hydrolase fold proteins.

Complete sequence of rabbit butyrylcholinesterase

Butyrylcholinesterase (E.C. 3.1.1.8) is present in all vertebrates (1, 2). We present here the sequence of rabbit BCHE gene deduced from three genomic clones described elsewhere (3). Each clone contained one exon and together covered the entire coding sequence. The structure of the rabbit BCHE gene is identical to the human gene (4) and to Torpedo ACHE gene (5). Positions of splicing sites within the coding sequence are conserved but non coding sequences are not conserved except for a portion of the 3 end untranslated sequence which may have a role in the regulation of the mRNA. The identity with human BCHE is 90.3% in nucleotidse over the coding sequence and 91.6% in amino acids. The high proportion of bases A and T is a characteristic of both human and rabbit BCHE gene. ACKNOWLEDGEMENTS

Kinetic parameters of cholinesterase interactions with organophosphates: retrieval and comparison tools available through ESTHER database

Cholinesterases are targets for organophosphorus compounds which are used as insecticides, chemical warfare agents and drugs for the treatment of disease such as glaucoma, or parasitic infections. The widespread use of these chemicals explains the growing of this area of research and the ever increasing number of sequences, structures, or biochemical data available. Future advances will depend upon effective management of existing information as well as upon creation of new knowledge. The ESTHER database goal is to facilitate retrieval and comparison of data about structure and function of proteins presenting the alpha/beta hydrolase fold. Protein engineering and in vitro production of enzymes allow direct comparison of biochemical parameters. Kinetic parameters of enzymatic reactions are now included in the database. These parameters can be searched and compared with a table construction tool. ESTHER can be reached through internet (http://www.ensam.inra.fr/cholinesterase). The full database or the specialised X-window Client-server system can be downloaded from our ftp server (ftp://ftp.toulouse.inra.fr./pub/esther). Forms can be used to send updates or corrections directly from the web.

ESTHER 1998, aChEdb Short Tutorial

ESTHER (for esterases, a/b hydrolase enzyme and relatives) is a database aimed at collecting in one information system, sequence data together with annotations. These include experimental biochemical results related to the structure-function analysis of the alpha/beta fold proteins. Description of the data base can be found in previous papers (1,2,3). Briefly sequences are separated in four groups: homologues of cholinesterases and carboxylesterases (BlockC), lipases (BlockL) mammalian hormone sensitive lipases and some bacterial esterases (BlockH) or alpha/beta fold proteins (BlockX).