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3  structures 19204  species 2  interactions 65322  sequences 52  architectures

Family: ABC_tran_Xtn (PF12848)

Summary: ABC transporter

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This is the Wikipedia entry entitled "ATP-binding domain of ABC transporters". More...

ATP-binding domain of ABC transporters Edit Wikipedia article

2hyd.png
Multidrug ABC transporter SAV1866, closed state
Identifiers
Symbol ABC_tran
Pfam PF00005
InterPro IPR003439
PROSITE PDOC00185
SCOP 1b0u
SUPERFAMILY 1b0u
TCDB 3.A.1
OPM superfamily 17
OPM protein 2hyd
CDD cd00267

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

ABC transporters belong to the ATP-Binding Cassette superfamily, which uses the hydrolysis of ATP to translocate a variety of compounds across biological membranes. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions 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.

Biological function

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.

Amino acid sequence

The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze 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 polarize the attacking 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.

3D structure

The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms.[1][2] 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.

Human proteins containing this domain

ABCA1; ABCA10; ABCA12; ABCA13; ABCA2; ABCA3; ABCA4; ABCA5; ABCA6; ABCA7; ABCA8; ABCA9; ABCB1; ABCB10; ABCB11; ABCB4; ABCB5; ABCB6; ABCB7; ABCB8; ABCB9; ABCC1; ABCC10; ABCC11; ABCC12; ABCC2; ABCC3; ABCC4; ABCC5; ABCC6; ABCC8; ABCC9; ABCD1; ABCD2; ABCD3; ABCD4; ABCE1; ABCF1; ABCF2; ABCF3; ABCG1; ABCG2; ABCG4; ABCG5; ABCG8; CFTR; MRP3; TAP1; TAP2; TAPL;

References

  1. ^ Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH (December 1998). "Crystal structure of the ATP-binding subunit of an ABC transporter". Nature 396 (6712): 703–7. doi:10.1038/25393. PMID 9872322. 
  2. ^ Hollenstein K, Dawson RJ, Locher KP (August 2007). "Structure and mechanism of ABC transporter proteins". Curr. Opin. Struct. Biol. 17 (4): 412–8. doi:10.1016/j.sbi.2007.07.003. PMID 17723295. 
  • Rosteck Jr, P. R.; Reynolds, P. A.; Hershberger, C. L. (1991). "Homology between proteins controlling Streptomyces fradiae tylosin resistance and ATP-binding transport". Gene 102 (1): 27–32. doi:10.1016/0378-1119(91)90533-h. PMID 1864505. 
  • Blight, M. A.; Holland, I. B. (1990). "Structure and function of haemolysin B,P-glycoprotein and other members of a novel family of membrane translocators". Molecular microbiology 4 (6): 873–880. doi:10.1111/j.1365-2958.1990.tb00660.x. PMID 1977073. 
  • Higgins, C. F.; Hyde, S. C.; Mimmack, M. M.; Gileadi, U.; Gill, D. R.; Gallagher, M. P. (1990). "Binding protein-dependent transport systems". Journal of bioenergetics and biomembranes 22 (4): 571–592. doi:10.1007/BF00762962. PMID 2229036. 

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This domain is an extension of some members of PF00005 and other ABC-transporter families.

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Domain organisation

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Alignments

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  Seed
(171)
Full
(65322)
Representative proteomes NCBI
(29705)
Meta
(1761)
RP15
(1209)
RP35
(3197)
RP55
(4758)
RP75
(6262)
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Format an alignment

  Seed
(171)
Full
(65322)
Representative proteomes NCBI
(29705)
Meta
(1761)
RP15
(1209)
RP35
(3197)
RP55
(4758)
RP75
(6262)
Alignment:
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Sequence:
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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
(171)
Full
(65322)
Representative proteomes NCBI
(29705)
Meta
(1761)
RP15
(1209)
RP35
(3197)
RP55
(4758)
RP75
(6262)
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

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_38684
Previous IDs: ABC_tran_2;
Type: Domain
Author: Mistry J
Number in seed: 171
Number in full: 65322
Average length of the domain: 86.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 14.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 85
Family (HMM) version: 3
Download: download the raw HMM for this family

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Archea Archea Eukaryota Eukaryota
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Interactions

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

ABC_tran ABC_tran

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_tran_Xtn domain has been found. There are 3 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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