PROSITE documentation PDOC00692
ABC transporter integral membrane type-2 domain profile


ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily which uses the hydrolysis of ATP to energize diverse biological import and export systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) (see <PDOC00185>) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein (mostly in eukaryotes and bacterial exporters) or on two different ones (mostly bacterial importers) [1,2,3]. But in a subgroup of exporters, the transmembrane region is encoded by a separated polypeptide, the ABC-2 type transport system integral membrane protein. The molecular size of this transmembrane protein is around 30 Kd. It is thought to contain six transmembrane regions, it either form homooligomeric channels or associate with another type of transmembrane protein to form heteroligomers. The function of the integral inner-membrane protein is to translocate the substrate across the membrane and seems to play an important role in substrate recognition [4].

The ABC-2 type transport system integral membrane proteins with a functional attribution are listed below:

  • Escherichia coli wzm (kpsM), involved in polysialic acid export.
  • Haemophilus influenzae bexB, involved in polyribosylribitol phosphate capsule polysaccharide export.
  • Neisseria meningitidis ctrC, involved in polyneuraminic acid capsule polysaccharide export.
  • Rhizobiacae nodulation protein J (gene nodJ), probably involved in exporting a modified β-1,4-linked N-acetylglucosamine oligosaccharide.
  • Streptomyces peucetius drrB, involved in exporting the antibiotics daunorubicin and Doxorubicin.
  • Klebsiella pneumoniae O-antigen export system protein rfbA.
  • Yersinia enterocolitica O-antigen export system protein rfbD.
  • Escherichia coli hypothetical protein yadH.
  • Escherichia coli hypothetical protein yhhJ.
  • Escherichia coli hypothetical protein yhih.

The profile we developed recognize the six transmembrane regions of ABC-2 integral membrane proteins.


These profile replaces a pattern (PS00890) whose specificity was inadequate. Furthermore, this profile matches some eukaryotic transporters in Drosophila melanogaster, Dictyostelium discoideum, Anopheles gambiae, and some prokaryotic fused exporters. None of these atypical matches are detected by other ABC TMD profiles (see <PDOC00364>).

Last update:

May 2005 / Text revised.


Technical section

PROSITE method (with tools and information) covered by this documentation:

ABC_TM2, PS51012; ABC transporter integral membrane type-2 domain profile  (MATRIX)


1AuthorsHolland I.B. Cole S.P.C. Kuchler K. Higgins C.F.
Source(In) ABC proteins from bacteria to man, Academic Press, San Diego, (2003).

2AuthorsHolland I.B. Blight M.A.
SourceJ. Mol. Biol. 293:381-399(1999).

3AuthorsSaurin W. Hofnung M. Dassa E.
TitleGetting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.
SourceJ. Mol. Evol. 48:22-41(1999).
PubMed ID9873074

4AuthorsAmbudkar S.V. Dey S. Hrycyna C.A. Ramachandra M. Pastan I. Gottesman M.M.
TitleBiochemical, cellular, and pharmacological aspects of the multidrug transporter.
SourceAnnu. Rev. Pharmacol. Toxicol. 39:361-398(1999).
PubMed ID10331089

5AuthorsReizer J. Reizer A. Saier M.H. Jr.
TitleA new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates.
SourceProtein Sci. 1:1326-1332(1992).
PubMed ID1303751

6AuthorsVazquez M. Santana O. Quinto C.
TitleThe NodL and NodJ proteins from Rhizobium and Bradyrhizobium strains are similar to capsular polysaccharide secretion proteins from gram-negative bacteria.
SourceMol. Microbiol. 8:369-377(1993).
PubMed ID8316086

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