Summary: ATP synthase alpha/beta family, beta-barrel domain
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ATP synthase alpha/beta subunits Edit Wikipedia article
| ATP synthase alpha/beta family, beta-barrel domain | |||||||||||
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| Identifiers | |||||||||||
| Symbol | ATP-synt_ab_N | ||||||||||
| Pfam | PF02874 | ||||||||||
| InterPro | IPR004100 | ||||||||||
| PROSITE | PDOC00137 | ||||||||||
| SCOP2 | 1bmf / SCOPe / SUPFAM | ||||||||||
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| ATP synthase alpha/beta family, nucleotide-binding domain | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | ATP-synt_ab | ||||||||||
| Pfam | PF00006 | ||||||||||
| InterPro | IPR000194 | ||||||||||
| PROSITE | PDOC00137 | ||||||||||
| SCOP2 | 1bmf / SCOPe / SUPFAM | ||||||||||
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| ATP synthase alpha/beta chain, C terminal domain | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | ATP-synt_ab_C | ||||||||||
| Pfam | PF00306 | ||||||||||
| InterPro | IPR000793 | ||||||||||
| SCOP2 | 1bmf / SCOPe / SUPFAM | ||||||||||
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ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness 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. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport[1][2].
- F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).
- V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles.
- A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases.
- P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.
- E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.
The alpha and beta (or A and B) subunits are found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively, as well as flagellar ATPase and the termination factor Rho. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis[3][4].
In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit[5].
In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.
The alpha/A and beta/B subunits can each be divided into three regions, or domains, centred around the ATP-binding pocket, and based on structure and function. The central domain contains the nucleotide-binding residues that make direct contact with the ADP/ATP molecule[6].
Human proteins containing this domain
ATP5A1; ATP5B; ATP6V1A; ATP6V1B1; ATP6V1B2;
References
- ^ Muller V, Cross RL (2004). "The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio". FEBS Lett. 576 (1): 1–4. PMID 15473999.
- ^ Zhang X, Niwa H, Rappas M (2004). "Mechanisms of ATPases--a multi-disciplinary approach". Curr Protein Pept Sci. 5 (2): 89–105. PMID 15078220.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Itoh H, Yoshida M, Yasuda R, Noji H, Kinosita K (2001). "Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase". Nature. 410 (6831): 898–904. PMID 11309608.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Wilkens S, Zheng Y, Zhang Z (2005). "A structural model of the vacuolar ATPase from transmission electron microscopy". Micron. 36 (2): 109–126. PMID 15629643.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Amzel LM, Bianchet MA, Leyva JA (2003). "Understanding ATP synthesis: structure and mechanism of the F1-ATPase (Review)". Mol. Membr. Biol. 20 (1): 27–33. PMID 12745923.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Chandler D, Wang H, Antes I, Oster G (2003). "The unbinding of ATP from F1-ATPase". Biophys. J. 85 (2): 695–706. PMID 12885621.
{{cite journal}}: CS1 maint: multiple names: authors list (link)
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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.
ATP synthase alpha/beta family, beta-barrel domain Provide feedback
This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.
Literature references
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Abrahams JP, Leslie AG, Lutter R, Walker JE; , Nature 1994;370:621-628.: Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. PUBMED:8065448 EPMC:8065448
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Shirakihara Y, Leslie AG, Abrahams JP, Walker JE, Ueda T, Sekimoto Y, Kambara M, Saika K, Kagawa Y, Yoshida M; , Structure 1997;5:825-836.: The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer. PUBMED:9261073 EPMC:9261073
Internal database links
| SCOOP: | ATP-synt_ab HAS-barrel |
External database links
| PROSITE: | PDOC00137 |
| SCOP: | 1bmf |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004100
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 F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [ PUBMED:11309608 , PUBMED:15629643 ].
In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit [ PUBMED:12745923 ].
In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.
The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain [ PUBMED:8065448 ]. This entry represents the N-terminal domain, which forms a closed beta-barrel with Greek-key topology.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Biological process | ATP metabolic process (GO:0046034) |
| proton transmembrane transport (GO:1902600) |
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 HAS-barrel (CL0275), which has the following description:
The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family [1].
The clan contains the following 2 members:
ATP-synt_ab_N HAS-barrelAlignments
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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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 (118) |
Full (30187) |
Representative proteomes | UniProt (150954) |
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| RP15 (4960) |
RP35 (15217) |
RP55 (29069) |
RP75 (46659) |
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| Jalview | |||||||
| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
— not available.
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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 (118) |
Full (30187) |
Representative proteomes | UniProt (150954) |
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|---|---|---|---|---|---|---|---|
| RP15 (4960) |
RP35 (15217) |
RP55 (29069) |
RP75 (46659) |
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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: |
Bateman A  , Sonnhammer ELL , Griffiths-Jones SR
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| Number in seed: | 118 |
| Number in full: | 30187 |
| Average length of the domain: | 67.4 aa |
| Average identity of full alignment: | 26 % |
| Average coverage of the sequence by the domain: | 13.29 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null 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: | 69 | ||||||||||||
| Family (HMM) version: | 26 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Bacteria
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Viruses
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Unclassified
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Viroids
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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 ATP-synt_ab_N domain has been found. There are 1795 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.
