Presentation of the database 

ABC systems petit triangle
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ABCISSE petit triangle
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 Introduction
ATP Binding Cassette (ABC) systems constitute one of the most abundant families of proteins. The most prominent characteristic of these systems is that they share a highly conserved ATPase domain, the ATP-binding cassette, which has been demonstrated to bind and hydrolyze ATP, thereby providing energy to a large number of biological processes. The amino acid sequence of this cassette displays three major conserved motifs, the Walker motifs A and B commonly found in ATPases and a specific signature motif also known as the linker peptide (
figure 1). The tertiary structure of the ABC domain is apparently conserved. The structural information for 2 ABC ATPases is available in the Protein Data Bank (click here for a comparison of the structures of HisP and MalK). We have identified more than 2000 ABC ATPase domains or proteins in translated nucleic acid sequence databases. A total of about 6000 proteins was found when the partners of ATPases were taken in account. The size of this mass of sequences is therefore similar to the coding capacity of a bacterial genome.
ABC systems are involved not only in the import or the export of a wide variety of substances, but also in many cellular processes and in their regulation.
Importers constitute mainly the prokaryotic subfamily of substrate-binding protein dependent transporters and their main function is to provide essential nutrients to bacteria even if the latter are present in submicromolar concentrations in the environment. Exporters are found in both prokaryotes and eukaryotes and are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. The third class of ABC systems is apparently not involved in transport but rather in cellular processes such as DNA repair, translation or regulation of gene expression.

Domain organization of ABC systems
ABC Transporters are composed of four structural domains: two very hydrophobic membrane spanning or integral membrane domains (IM) and two hydrophilic cytoplasmic domains carrying the ATP-binding cassette (ABC) and peripherally associated to IM on the cytosolic side of the membrane.
    
Importers have in general the four domains carried by independent polypeptides and they need for optimal function an extracellular substrate-binding protein. This protein, an essential component for transport, is a periplasmic protein in Gram-negative bacteria and a surface-anchored lipoprotein in Gram-positive bacteria and archaea (figure 2).
    
Exporters have the four domains fused in several ways. Prokaryote exporters have the IM domain fused to the ABC domain (IM-ABC) and require additional proteins for function. In general, they need a cytoplasmic membrane component belonging to the membrane fusion protein (MFP) family and in Gram-negative bacteria an outer membrane protein. Eukaryote exporters are similar to prokaryote exporters in their design. However, some eukaryote families of exporters display the four domains on the same polypeptide chain ((IM-ABC)2) (figure 3).
    
Systems involved in cellular processes other than transport do not have IM domains and are comprised of duplicated and fused ABC domains (ABC2) (figure 4)

Presentation of the database
The ABCISSE database is the result of a phylogenetic and functional classification of ABC systems found in living organisms. The central objet of the database is the system, which is comprised of a set of proteins (called also partners) known or predicted to function together in order to accomplish a specific function. The database is comprised of about 2000 systems and this number is expected to increase very quickly since 10 to 30 new systems are submitted to sequence databases every month. Systems whose members display a strong primary sequence conservation are grouped in families, which may be divided in subfamilies. The database is comprised of 34 families. In most cases, systems from a given family are performing similar functions. Families are grouped in three phylogenetic classes which fit fairly well wiht the three fuctional categories which are Import, Export and Non Transport Cellular processes.
The classification is based primarily on two phylogenetic analyses of the sequences of the highly conserved ATPase subunit or domain shared by ABC sytems. The first analysis was concucted with a set of about 200 sequences (
Saurin et al, 1999). A second round of analyzes was performed with about 600 sequences from completely sequenced organisms. The results of the studies were consistent with a very early segregation of the three functional categories within the common ancestor of living organisms. Additional classifications were performed on the partners of transport systems and it was found that the classifications of ABC ATPases and those of their partners were generally similar. This behaviour suggests that ABC systems evolve as a whole entity with little shuffling of domains and partners during evolvution.

Navigating in the database
The "Quick look-up" section :
This section is intended to help retrieving quickly a peculiar ABC system. A system can be accessed from the name of the organism, from the name of the family to which it belongs, from the name of the transported substrate, or from the gene name of one of the partners that constitute the system.

The "List of species" search :
This is a list of organisms known to carry at least 1 ABC system and its was broken into several sub-lists for a compact display. The species are sorted according to the initial of the genus. The list gives the number of ABC systems described in the organisms and reports if the genome is completely sequenced. Click on the "Organism" name to display the list of the ABC systems identified in this organism. Then click of the "Family" name to display a view of the system (see below for additional help). Alternatively, click on the "Substrate" name to display a list of organisms known to contain a system specific for this substrate.

The "List of families" search :
This is a list of families sorted according to the physiological function of the systems (Export, Cellular processes, Import, or Unknown). The abbreviated name of the family is explained in the "Definition" column. Click on the "Family" name or on the "Sub-family" name to display a list of "Species" (organisms) known to possess at least 1 member of this family or subfamily. This list provides for each species the name of the substrate handled by the ABC system and if it is not known, the biological role played by this system. Click on "details" to display a brief overview of the properties of the family or sub-family.
Click on the "Species" name to display a view of the system.
Alternatively, click on the "Substrate" name to display a list of organisms known to contain a system specific for this substrate.

The "List of substrates" search
This is an alphabetical list of substrates known to be transported by an ABC system. Click on the "Substrate" name to display a list of organisms known to transport this molecule. Click on the "Family" name to display all the members of the family comprising this system.

The "gene name" search :
Enter the name of the gene to search and click on the submit button

2. The "Advanced search" section: under construction

3. The phylogenetic tree section: under construction

Viewing ABC systems:
The complete description of a system is presented on several pages. The first page "View of ABC system" provides an overview of the properties of the system and a list of its constituents (partners). Each partner of a system is described on the "View of ABC partner" pages which can be accessed by clicking on the name of the partner.

The "View of ABC system" page provides the following information:

 General information on the system
 Abcisse Accession Number   Internal reference
 Entered in ABCISSE in   Internal reference
 Last modification   Internal reference
 Fonction (status * )   Biological function of the system, this could be Import, Export or Cellular processes (e.g. DNA repair)
 Family   A series of systems with clear primary sequence similarity   (details **)
 Sub-family   A series of systems with clear primary sequence and functional similarity   (details **)
 Substrate (status * )   Molecule transported by a given system  
 Role (status * )  Physiological function of ABC systems not involved in transport (e.g. DNA repair)
OR
 Physiological function of a putative transport system whose substrate is unknown (e.g. fimbriae formation)  
 Associated disease(s)    Human disease(s) determined by a mutation in a system
 Organism   Genus and species names of the organism  
 Taxonomy   Taxonomic position of the organism
 References
  [1]   Selected bibliography documenting the function of the system
 Comments
   Some particular features of the system

 Structure of System  (gene name)

  This section gives the list and the organization of the genes that constitute the system. Click on the gene name to display the properties of the gene

 *  The "status" field indicates whether a given function, substrate specificity or role of a system is predicted or experimentally verified 
 **  The "details" field gives a brief overview of the properties of the family or sub-family.

The "View of ABC partner" page provides the following information:

  Partner
  Type   Domain organization of the partner (see above for the definition of the symbols)
  GI   NCBI unique identifier and link to the GenPept format of the translated gene
  Gene name   
  Strain  
  DNA  Subcellular location (Chromosome, plasmid, plastid, etc.)
  Location absolute  Coordinates of the gene on the genome
  Location relative  Coordinates of the gene on the contig
  [Comp.]   (Join)  [C-]   (J- )
  Accession number   Database accession number and link to the Genbank format
  DB name : ID   Database name and database unique identifier of the gene
  Length     a.a. Molecular Weight     Seq. Fasta
  Motif(s)   Characteristic sequence motifs
  Comments   Some particular features of the partner
 

Synonym(s)   List of (and links to) identical sequences in different databases
 
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