Summary: ABC transporter
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This is the Wikipedia entry entitled "ATP-binding cassette transporter". More...
ATP-binding cassette transporter Edit Wikipedia article
'ATP binding cassette (ABC) transporters are transporting various material over membranes, for example the inner mitochondrial membrane.
Category: Biology->Biochemistry/Microbiology
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This is the Wikipedia entry entitled "ATP-binding domain of ABC transporters". More...
ATP-binding domain of ABC transporters Edit Wikipedia article
| ABC transporter | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | ? | ||||||||||
| Pfam | PF00005 | ||||||||||
| InterPro | IPR003439 | ||||||||||
| PROSITE | PDOC00185 | ||||||||||
| SCOP2 | 1b0u / SCOPe / SUPFAM | ||||||||||
| TCDB | 3.A.1 | ||||||||||
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ATP-binding domain of ABC transporters is a water-soluble domain of transmembrane ABC transporters.
ABC transporters belong to the ATP-Binding Cassette (ABC) 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.
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.
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 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.
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.
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] PMIDÂ 1864505 Homology between proteins controlling Streptomyces fradiae tylosin resistance and ATP-binding transport. Rosteck PR Jr, Reynolds PA, Hershberger CL; Gene 1991;102:27-32.
- [ 2] PMIDÂ 1977073 Structure and function of haemolysin B,P-glycoprotein and other members of a novel family of membrane translocators. Blight MA, Holland IB; Mol Microbiol 1990;4:873-880.
- [ 3] PMIDÂ 2229036 Binding protein-dependent transport systems. Higgins CF, Hyde SC, Mimmack MM, Gileadi U, Gill DR, Gallagher MP; J Bioenerg Biomembr 1990;22:571-592.
- [ 4] PMIDÂ 9872322 Crystal structure of the ATP-binding subunit of an ABC transporter. Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH; Nature 1998;396:703-707.
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 Provide feedback
ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain PF00664. These four domains may belong to a single polypeptide as in P13569 or belong in different polypeptide chains.
Literature references
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Rosteck PR Jr, Reynolds PA, Hershberger CL; , Gene 1991;102:27-32.: Homology between proteins controlling Streptomyces fradiae tylosin resistance and ATP-binding transport. PUBMED:1864505 EPMC:1864505
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Blight MA, Holland IB; , Mol Microbiol 1990;4:873-880.: Structure and function of haemolysin B,P-glycoprotein and other members of a novel family of membrane translocators. PUBMED:1977073 EPMC:1977073
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Higgins CF, Hyde SC, Mimmack MM, Gileadi U, Gill DR, Gallagher MP; , J Bioenerg Biomembr 1990;22:571-592.: Binding protein-dependent transport systems. PUBMED:2229036 EPMC:2229036
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Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH; , Nature 1998;396:703-707.: Crystal structure of the ATP-binding subunit of an ABC transporter. PUBMED:9872322 EPMC:9872322
Internal database links
External database links
| HOMSTRAD: | ABC_tran |
| PROSITE: | PDOC00185 |
| SCOP: | 1b0u |
| Transporter classification: | 3.A.1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003439
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 ].
On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [ PUBMED:2229036 , PUBMED:3288195 , PUBMED:3762694 , PUBMED:3762695 , PUBMED:1977073 ].
The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [ PUBMED:6329717 ] or the 'P-loop' [ PUBMED:2126155 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | ATP binding (GO:0005524) |
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 P-loop_NTPase (CL0023), which has the following description:
AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].
The clan contains the following 245 members:
6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR BrxC_BrxD BrxL_ATPase Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin ZotAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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| Seed (55) |
Full (838816) |
Representative proteomes | UniProt (3489531) |
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| RP15 (103125) |
RP35 (389049) |
RP55 (832238) |
RP75 (1428870) |
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| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (55) |
Full (838816) |
Representative proteomes | UniProt (3489531) |
||||
|---|---|---|---|---|---|---|---|
| RP15 (103125) |
RP35 (389049) |
RP55 (832238) |
RP75 (1428870) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
| Seed source: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Sonnhammer ELL  , Bateman A
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| Number in seed: | 55 |
| Number in full: | 838816 |
| Average length of the domain: | 148.5 aa |
| Average identity of full alignment: | 26 % |
| Average coverage of the sequence by the domain: | 36.68 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 137 | ||||||||||||
| Family (HMM) version: | 30 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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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 domain has been found. There are 1197 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
