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691  structures 8124  species 0  interactions 10605  sequences 58  architectures

Family: ATP-synt_ab_C (PF00306)

Summary: ATP synthase alpha/beta chain, C terminal domain

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 "ATP synthase alpha/beta subunits". More...

ATP synthase alpha/beta subunits Edit Wikipedia article

ATP synthase alpha/beta family, beta-barrel domain
Identifiers
SymbolATP-synt_ab_N
PfamPF02874
InterProIPR004100
PROSITEPDOC00137
SCOP21bmf / SCOPe / SUPFAM
ATP synthase alpha/beta family, nucleotide-binding domain
Identifiers
SymbolATP-synt_ab
PfamPF00006
InterProIPR000194
PROSITEPDOC00137
SCOP21bmf / SCOPe / SUPFAM
ATP synthase alpha/beta chain, C terminal domain
Identifiers
SymbolATP-synt_ab_C
PfamPF00306
InterProIPR000793
SCOP21bmf / SCOPe / SUPFAM

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

  1. ^ 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.
  2. ^ 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)
  3. ^ 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)
  4. ^ 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)
  5. ^ 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)
  6. ^ 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)
This article incorporates text from the public domain Pfam and InterPro: IPR000194

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.

ATP synthase alpha/beta chain, C terminal domain Provide feedback

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Literature references

  1. 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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000793

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 of 7 and 6 helices, respectively, in the alpha and beta subunits [ PUBMED:8065448 ]. This entry represents the C-terminal domain of the alpha subunit.

Gene Ontology

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Domain organisation

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Alignments

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(179)
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(5187)
RP55
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RP75
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(179)
Full
(10605)
Representative proteomes UniProt
(57244)
RP15
(1602)
RP35
(5187)
RP55
(10447)
RP75
(17183)
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  Seed
(179)
Full
(10605)
Representative proteomes UniProt
(57244)
RP15
(1602)
RP35
(5187)
RP55
(10447)
RP75
(17183)
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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

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: Pfam-B_15 (release 1.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 179
Number in full: 10605
Average length of the domain: 123.7 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 24.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 27.0
Noise cut-off 26.8 26.9
Model length: 126
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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_C domain has been found. There are 691 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.

Protein Predicted structure External Information
A0A044S1L6 View 3D Structure Click here
A0A077Z929 View 3D Structure Click here
A0A077ZF69 View 3D Structure Click here
A0A077ZK51 View 3D Structure Click here
A0A077ZLS7 View 3D Structure Click here
A0A0D2GYZ8 View 3D Structure Click here
A0A0G2K099 View 3D Structure Click here
A0A0H3GZ37 View 3D Structure Click here
A0A0K0E463 View 3D Structure Click here
A0A0K0IZ73 View 3D Structure Click here
A0A0R0FZZ9 View 3D Structure Click here
A0A0R0HDS5 View 3D Structure Click here
A0A0R0JZ78 View 3D Structure Click here
A0A175VRU2 View 3D Structure Click here
A0A1C1CL99 View 3D Structure Click here
A0A1D8PDC4 View 3D Structure Click here
A0A1X7YHF8 View 3D Structure Click here
A0A2P2CLF9 View 3D Structure Click here
A0A3P7FR98 View 3D Structure Click here
A0A3P7QA10 View 3D Structure Click here
A0JY66 View 3D Structure Click here
A0KQY0 View 3D Structure Click here
A0LDA2 View 3D Structure Click here
A0LLG0 View 3D Structure Click here
A0LSL4 View 3D Structure Click here
A0Q2Z6 View 3D Structure Click here
A0R202 View 3D Structure Click here
A0T0F1 View 3D Structure Click here
A0T0P4 View 3D Structure Click here
A1A3C7 View 3D Structure Click here
A1ALL5 View 3D Structure Click here
A1AXU4 View 3D Structure Click here
A1B8N8 View 3D Structure Click here
A1BJF5 View 3D Structure Click here
A1E9S1 View 3D Structure Click here
A1K1S0 View 3D Structure Click here
A1R7V5 View 3D Structure Click here
A1SBU2 View 3D Structure Click here
A1SHI9 View 3D Structure Click here
A1SS62 View 3D Structure Click here