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0  structures 1284  species 0  interactions 2221  sequences 15  architectures

Family: ABC_membrane_2 (PF06472)

Summary: ABC transporter transmembrane region 2

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]

Contents

[edit] Subfamilies

[edit] Human proteins containing this domain

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;

[edit] References

  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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC305842/.
  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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC125601/.

[edit] External links


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 2 Provide feedback

This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with PF00664. Mutations in this domain in P28288 are believed responsible for Zellweger Syndrome-2 [1]; mutations in P33897 are responsible for recessive X-linked adrenoleukodystrophy [2]. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids [3].

Literature references

  1. Gartner J, Moser H, Valle D; , Nat Genet 1992;1:16-23.: Mutations in the 70K peroxisomal membrane protein gene in Zellweger syndrome. PUBMED:1301993 EPMC:1301993

  2. Mosser J, Douar AM, Sarde CO, Kioschis P, Feil R, Moser H, Poustka AM, Mandel JL, Aubourg P; , Nature 1993;361:726-730.: Putative X-linked adrenoleukodystrophy gene shares unexpected homology with ABC transporters. PUBMED:8441467 EPMC:8441467

  3. Hettema EH, van Roermund CW, Distel B, van den Berg M, Vilela C, Rodrigues-Pousada C, Wanders RJ, Tabak HF; , EMBO J 1996;15:3813-3822.: The ABC transporter proteins Pat1 and Pat2 are required for import of long-chain fatty acids into peroxisomes of Saccharomyces cerevisiae. PUBMED:8670886 EPMC:8670886


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010509

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).

This region covers the N terminus and first two membrane regions of a small family of ABC transporters. Mutations in this domain in SWISSPROT are believed responsible for Zellweger Syndrome-2 [PUBMED:1301993]; mutations in SWISSPROT are responsible for recessive X-linked adrenoleukodystrophy [PUBMED:8441467]. A Saccharomyces cerevisiae protein containing this domain is involved in the import of long-chain fatty acids [PUBMED:8670886].

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
(26)
Full
(2221)
Representative proteomes NCBI
(2380)
Meta
(1271)
RP15
(255)
RP35
(477)
RP55
(704)
RP75
(895)
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Format an alignment

  Seed
(26)
Full
(2221)
Representative proteomes NCBI
(2380)
Meta
(1271)
RP15
(255)
RP35
(477)
RP55
(704)
RP75
(895)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(26)
Full
(2221)
Representative proteomes NCBI
(2380)
Meta
(1271)
RP15
(255)
RP35
(477)
RP55
(704)
RP75
(895)
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.

Pfam alignments:

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: ADDA_6479
Previous IDs: Ald_N;
Type: Family
Author: Yeats C
Number in seed: 26
Number in full: 2221
Average length of the domain: 271.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 45.53 %

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 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 282
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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