ABCdb

Last updated
ABCdb
Content
DescriptionABCdb database on ABC transporter systems in prokaryotic genomes.
Data types
captured
ATP-binding Cassette (ABC) transporters
Organisms prokaryotes
Contact
Research center University of Toulouse, CNRS
Laboratory LMGM
Primary citation PMID   16499625
Access
Website http://www-abcdb.biotoul.fr/
Tools
Web advanced search, BLAST
Miscellaneous
Curation policyyes - automatic and manual
Bookmarkable
entities
yes

ABCdb is a biological database for the adenosine triphosphate-binding cassette (ABC) transporters encoded by completely sequenced archaeal and bacterial genomes. These proteins are important for transporting substances into cells and are found in all living organisms.

Contents

biological function of ABC systems

Most ABC systems function in the transport of a compound across a membrane into the cell (importer) or to the exterior (exporter), for which the system generates energy by the hydrolysis of adenosine triphosphate (ATP). The ABC transporters occur in all living organisms.

An ABC transporter system consist minimally of two components: an ATP binding cassette and a transmembrane domain or membrane spanning domain. These are usually separate proteins or can occur as protein domains. A typical ABC transporter is composed of two nucleotide binding domains that energize transport via ATP hydrolysis and of two membrane spanning domains that act as a membrane channel for the substrate. Importers require a solute binding protein that recognizes and binds the substrate.

The different partners of an ABC system are generally encoded by neighboring genes.

Features

The ABC proteins form a protein superfamily encoded by large families of paralogous genes. Sequence analysis shows that members of the ABC superfamily may have diverged from common ancestral forms and permits to organize ABC proteins into sub-families. The classification of ABC systems into (sub-)families can help to predict which substrates may be transported by the system.

ABCdb is a public resource, [1] from which one can:

See also

Related Research Articles

<span class="mw-page-title-main">ATPase</span> Dephosphorylation enzyme

ATPases (EC 3.6.1.3, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3-ATPase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or the inverse reaction. This dephosphorylation reaction releases energy, which the enzyme (in most cases) harnesses to drive other chemical reactions that would not otherwise occur. This process is widely used in all known forms of life.

A membrane transport protein is a membrane protein involved in the movement of ions, small molecules, and macromolecules, such as another protein, across a biological membrane. Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport. The two main types of proteins involved in such transport are broadly categorized as either channels or carriers. The solute carriers and atypical SLCs are secondary active or facilitative transporters in humans. Collectively membrane transporters and channels are known as the transportome. Transportomes govern cellular influx and efflux of not only ions and nutrients but drugs as well.

<span class="mw-page-title-main">ATP-binding cassette transporter</span> Gene family

The ATP-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.

<span class="mw-page-title-main">Efflux (microbiology)</span> Protein complexes that move compounds, generally toxic, out of bacterial cells

In microbiology, efflux is the moving of a variety of different compounds out of cells, such as antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals, bacterial metabolites and neurotransmitters. All microorganisms, with a few exceptions, have highly conserved DNA sequences in their genome that encode efflux pumps. Efflux pumps actively move substances out of a microorganism, in a process known as active efflux, which is a vital part of xenobiotic metabolism. This active efflux mechanism is responsible for various types of resistance to bacterial pathogens within bacterial species - the most concerning being antibiotic resistance because microorganisms can have adapted efflux pumps to divert toxins out of the cytoplasm and into extracellular media.

Translocase is a general term for a protein that assists in moving another molecule, usually across a cell membrane. These enzymes catalyze the movement of ions or molecules across membranes or their separation within membranes. The reaction is designated as a transfer from “side 1” to “side 2” because the designations “in” and “out”, which had previously been used, can be ambiguous. Translocases are the most common secretion system in Gram positive bacteria.

<span class="mw-page-title-main">ABCG2</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette super-family G member 2 is a protein that in humans is encoded by the ABCG2 gene. ABCG2 has also been designated as CDw338. ABCG2 is a translocation protein used to actively pump drugs and other compounds against their concentration gradient using the bonding and hydrolysis of ATP as the energy source.

<span class="mw-page-title-main">ATP-binding domain of ABC transporters</span> Water-soluble domain of transmembrane ABC transporters

In molecular biology, ATP-binding domain of ABC transporters is a water-soluble domain of transmembrane ABC transporters.

<span class="mw-page-title-main">P-type ATPase</span>

The P-type ATPases, also known as E1-E2 ATPases, are a large group of evolutionarily related ion and lipid pumps that are found in bacteria, archaea, and eukaryotes. P-type ATPases are α-helical bundle primary transporters named based upon their ability to catalyze auto- (or self-) phosphorylation (hence P) of a key conserved aspartate residue within the pump and their energy source, adenosine triphosphate (ATP). In addition, they all appear to interconvert between at least two different conformations, denoted by E1 and E2. P-type ATPases fall under the P-type ATPase (P-ATPase) Superfamily (TC# 3.A.3) which, as of early 2016, includes 20 different protein families.

<span class="mw-page-title-main">ABCA4</span> Mammalian protein found in Homo sapiens

ATP-binding cassette, sub-family A (ABC1), member 4, also known as ABCA4 or ABCR, is a protein which in humans is encoded by the ABCA4 gene.

<span class="mw-page-title-main">ABCA2</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family A member 2 is a protein that in humans is encoded by the ABCA2 gene.

<span class="mw-page-title-main">ABCB9</span> Protein-coding gene in humans

ATP-binding cassette sub-family B member 9 is a protein that in humans is encoded by the ABCB9 gene.

<span class="mw-page-title-main">ABCA3</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family A member 3 is a protein that in humans is encoded by the ABCA3 gene.

<span class="mw-page-title-main">ABCB7</span> Protein-coding gene in humans

ATP-binding cassette sub-family B member 7, mitochondrial is a protein that in humans is encoded by the ABCB7 gene.

<span class="mw-page-title-main">ABCF1</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family F member 1 is a protein that in humans is encoded by the ABCF1 gene.

<span class="mw-page-title-main">ABCD4</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family D member 4 is a protein that in humans is encoded by the ABCD4 gene.

<span class="mw-page-title-main">ABCB8</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family B member 8, mitochondrial is a protein that in humans is encoded by the ABCB8 gene.

<span class="mw-page-title-main">ABCC12</span> Protein-coding gene in the species Homo sapiens

Multidrug resistance-associated protein 9 is a protein that in humans is encoded by the ABCC12 gene.

<span class="mw-page-title-main">ABCA9</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family A member 9 is a protein that in humans is encoded by the ABCA9 gene.

<span class="mw-page-title-main">ABCE1</span> Protein-coding gene in the species Homo sapiens

ATP-binding cassette sub-family E member 1 (ABCE1) also known as RNase L inhibitor (RLI) is an enzyme that in humans is encoded by the ABCE1 gene.

Arsenite resistance (Ars) efflux pumps of bacteria may consist of two proteins, ArsB and ArsA, or of one protein. ArsA proteins have two ATP binding domains and probably arose by a tandem gene duplication event. ArsB proteins all possess twelve transmembrane spanners and may also have arisen by a tandem gene duplication event. Structurally, the Ars pumps resemble ABC-type efflux pumps, but there is no significant sequence similarity between the Ars and ABC pumps. When only ArsB is present, the system operates by a pmf-dependent mechanism, and consequently belongs in TC subclass 2.A. When ArsA is also present, ATP hydrolysis drives efflux, and consequently the system belongs in TC subclass 3.A. ArsB therefore appears twice in the TC system but ArsA appears only once. These pumps actively expel both arsenite and antimonite.

References

  1. Fichant G, Basse MJ, Quentin Y (Mar 2006). "ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes". FEMS Microbiology Letters. 256 (2): 333–9. doi:10.1111/j.1574-6968.2006.00139.x. PMID   16499625.