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28  structures 5230  species 2  interactions 51056  sequences 190  architectures

Family: ABC_membrane (PF00664)

Summary: ABC transporter transmembrane region

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Transmembrane domain of ABC transporters". More...

Transmembrane domain of ABC transporters Edit Wikipedia article

ABC transporter transmembrane region
Identifiers
Symbol ABC_membrane
Pfam PF00664
InterPro IPR001140
PROSITE PDOC00364
SCOP 1pf4
SUPERFAMILY 1pf4
TCDB 3.A.1
OPM superfamily Lipid/drug exporters 1.1.10.03. Lipid/drug exporters
OPM protein 2hyd

ABC transporter transmembrane domain is main transmembrane structural unit of ATP-binding cassette transporter which consist of six transmembrane domaines. Many members of the ABC transporter family (Pfam PF00005) have two such regions.[1][2][3][4][5][6]

Subfamilies[edit]

Human proteins containing this domain[edit]

ABCB1; ABCB10; ABCB11; ABCB4; ABCB5; ABCB6; ABCB7; ABCB8; ABCB9; ABCC1; ABCC10; ABCC11; ABCC12; ABCC13; ABCC2; ABCC3; ABCC4; ABCC5; ABCC6; ABCC8; ABCC9; CFTR; TAP1; TAP2; TAPL;

References[edit]

  1. ^ Kerr ID (2002). "Structure and association of ATP-binding cassette transporter nucleotide-binding domains". Biochim. Biophys. Acta 1561 (1): 47–64. PMID 11988180. 
  2. ^ Hunt JF, Yuan YR, Martsinkevich O, Millen L, Thomas PJ, Karpowich N, Dai PL, MacVey K (2001). "Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter". Structure 9 (7): 571–86. doi:10.1016/S0969-2126(01)00617-7. PMID 11470432. 
  3. ^ Hunt JF, Yuan YR, Blecker S, Martsinkevich O, Millen L, Thomas PJ (2001). "The crystal structure of the MJ0796ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter". J. Biol. Chem. 276 (34): 32313–21. doi:10.1074/jbc.M100758200. PMID 11402022. 
  4. ^ Kim SH, Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF (1998). "Crystal structure of the ATP-binding subunit of an ABC transporter". Nature 396 (6712): 703–707. doi:10.1038/25393. PMID 9872322. 
  5. ^ Welte W, Breed J, Boos W, Diederichs K, Vonrhein C, Muller C, Diez J, Greller G, Schnell C (2000). "Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis". EMBO J. 19 (22): 5951–61. doi:10.1093/emboj/19.22.5951. PMC 305842. PMID 11080142. 
  6. ^ Wiley DC, Gaudet R (2001). "Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing". EMBO J. 20 (17): 4964–72. doi:10.1093/emboj/20.17.4964. PMC 125601. PMID 11532960. 

External links[edit]


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

ABC transporter transmembrane region Provide feedback

This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (PF00005) have two such regions.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001140

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.

ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain [PUBMED:9873074].

The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [PUBMED:11421269, PUBMED:1282354, PUBMED:9640644].

The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [PUBMED:11988180, PUBMED:11470432, PUBMED:11402022, PUBMED:9872322, PUBMED:11080142, PUBMED:11532960].

The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions [PUBMED:9873074]. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [PUBMED:9873074, PUBMED:11421270]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [PUBMED:9873074, PUBMED:11421269, PUBMED:11421270]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).

A variety of ATP-binding transport proteins have a six transmembrane helical region. They are all integral membrane proteins involved in a variety of transport systems. Members of this family include; the cystic fibrosis transmembrane conductance regulator (CFTR), bacterial leukotoxin secretion ATP-binding protein, multidrug resistance proteins, the yeast leptomycin B resistance protein, the mammalian sulphonylurea receptor and antigen peptide transporter 2. Many of these proteins have two such regions.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan ABC_membrane (CL0241), which has the following description:

This clan includes families that are the membrane components of ABC transporter complexes. In general these regions are composed of six transmembrane helices [1].

The clan contains the following 4 members:

ABC_membrane ABC_membrane_2 ABC_membrane_3 SbmA_BacA

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(70)
Full
(51056)
Representative proteomes NCBI
(42384)
Meta
(7093)
RP15
(5333)
RP35
(9845)
RP55
(13729)
RP75
(16541)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(70)
Full
(51056)
Representative proteomes NCBI
(42384)
Meta
(7093)
RP15
(5333)
RP35
(9845)
RP55
(13729)
RP75
(16541)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(70)
Full
(51056)
Representative proteomes NCBI
(42384)
Meta
(7093)
RP15
(5333)
RP35
(9845)
RP55
(13729)
RP75
(16541)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_2 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 70
Number in full: 51056
Average length of the domain: 265.40 aa
Average identity of full alignment: 13 %
Average coverage of the sequence by the domain: 43.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 275
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

ABC_tran ABC_membrane

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ABC_membrane domain has been found. There are 28 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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