Summary: ATP synthase subunit D
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ATP synthase subunit D Provide feedback
This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase [2].
Literature references
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Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V; , J Biol Chem 1996;271:18843-18852.: Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. PUBMED:8702544 EPMC:8702544
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Nelson H, Mandiyan S, Nelson N; , Proc Natl Acad Sci U S A 1995;92:497-501.: A bovine cDNA and a yeast gene (VMA8) encoding the subunit D of the vacuolar H(+)-ATPase. PUBMED:7831318 EPMC:7831318
This tab holds annotation information from the InterPro database.
InterPro entry IPR002699
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [PUBMED:15473999, PUBMED:15078220]. The different types include:
- F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).
- V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [PUBMED:20450191]. They are also found in bacteria [PUBMED:9741106].
- A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [PUBMED:18937357, PUBMED:1385979].
- P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.
- E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.
The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [PUBMED:11309608, PUBMED:15629643, PUBMED:15168615]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases.
This is a family of D subunits from various ATP synthases, including V-type H+ transporting and Na+ transporting [PUBMED:8157629]. This family is found in eukaryota, bacteria and archaea [PUBMED:10788522, PUBMED:9177272]. The V-type ATPase can use a proton gradient to synthesize ATP, but the primary biological role is to acidify some compartment, such as yeast vacuole (a lysosomal homologous) or the interior of a prokaryote. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase [PUBMED:7831318].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | ATPase-coupled transmembrane transporter activity (GO:0042626) |
Domain organisation
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Alignments
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Seed (282) |
Full (2962) |
Representative proteomes | UniProt (9060) |
NCBI (8682) |
Meta (150) |
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RP15 (574) |
RP35 (1549) |
RP55 (2477) |
RP75 (3824) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (282) |
Full (2962) |
Representative proteomes | UniProt (9060) |
NCBI (8682) |
Meta (150) |
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RP15 (574) |
RP35 (1549) |
RP55 (2477) |
RP75 (3824) |
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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.
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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
Seed source: | Pfam-B_1304 (release 4.2) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 282 |
Number in full: | 2962 |
Average length of the domain: | 184.00 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 80.01 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 196 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 4 interactions for this family. More...
ATP-synt_ab_C ATP-synt_F vATP-synt_AC39 ATP-synt_abStructures
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 ATP-synt_D domain has been found. There are 41 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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