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	PROSITE documentation PDOC00692

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.

Note:

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.

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

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

• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 164
  • detected by PS51012: 42 (true positives)
  • undetected by PS51012: 122 (122 false negatives and 0 'partial')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS51012:
  NONE.
• Domain architecture view of Swiss-Prot proteins matching PS51012
  
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51012
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51012
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS51012
• View ligand binding statistics of PS51012

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

2	Authors	Holland I.B., Blight M.A.
	Source	J. Mol. Biol. 293:381-399(1999).

3	Authors	Saurin W., Hofnung M., Dassa E.
	Title	Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.
	Source	J. Mol. Evol. 48:22-41(1999).
	PubMed ID	9873074

4	Authors	Ambudkar S.V., Dey S., Hrycyna C.A., Ramachandra M., Pastan I., Gottesman M.M.
	Title	Biochemical, cellular, and pharmacological aspects of the multidrug transporter.
	Source	Annu. Rev. Pharmacol. Toxicol. 39:361-398(1999).
	PubMed ID	10331089
	DOI	10.1146/annurev.pharmtox.39.1.361

5	Authors	Reizer J., Reizer A., Saier M.H. Jr.
	Title	A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates.
	Source	Protein Sci. 1:1326-1332(1992).
	PubMed ID	1303751

6	Authors	Vazquez M., Santana O., Quinto C.
	Title	The NodL and NodJ proteins from Rhizobium and Bradyrhizobium strains are similar to capsular polysaccharide secretion proteins from gram-negative bacteria.
	Source	Mol. Microbiol. 8:369-377(1993).
	PubMed ID	8316086

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