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496  structures 27612  species 16  interactions 61020  sequences 81  architectures

Family: ATP-synt_ab_N (PF02874)

Summary: ATP synthase alpha/beta family, beta-barrel domain

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This is the Wikipedia entry entitled "ATP synthase alpha/beta subunits". More...

ATP synthase alpha/beta subunits Edit Wikipedia article

A part of F1 ATP synthase complex: alpha, beta and gamma subunits (PDB: 1bmf​)
ATP synthase alpha/beta family, beta-barrel domain
Symbol ATP-synt_ab_N
Pfam PF02874
InterPro IPR004100
SCOP 1bmf
ATP synthase alpha/beta family, nucleotide-binding domain
Symbol ATP-synt_ab
Pfam PF00006
InterPro IPR000194
SCOP 1bmf
ATP synthase alpha/beta chain, C terminal domain
Symbol ATP-synt_ab_C
Pfam PF00306
InterPro IPR000793
SCOP 1bmf

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 nucleoside triphosphates, 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 on 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



  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. doi:10.1016/j.febslet.2004.08.065. 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. doi:10.2174/1389203043486874. PMID 15078220. 
  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. doi:10.1038/35073513. PMID 11309608. 
  4. ^ Wilkens S, Zheng Y, Zhang Z (2005). "A structural model of the vacuolar ATPase from transmission electron microscopy". Micron 36 (2): 109–126. doi:10.1016/j.micron.2004.10.002. PMID 15629643. 
  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. doi:10.1080/0968768031000066532. PMID 12745923. 
  6. ^ Chandler D, Wang H, Antes I, Oster G (2003). "The unbinding of ATP from F1-ATPase". Biophys. J. 85 (2): 695–706. doi:10.1016/S0006-3495(03)74513-5. PMC 1303195. PMID 12885621. 

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 family, beta-barrel domain Provide feedback

This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.

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

  2. 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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004100

F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [PUBMED:11309608]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

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.

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-barrel


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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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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.

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Bateman A, Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 133
Number in full: 61020
Average length of the domain: 66.80 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 14.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 19.0
Trusted cut-off 20.9 19.0
Noise cut-off 20.8 18.9
Model length: 69
Family (HMM) version: 19
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Species distribution

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Colour assignments

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


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There are 16 interactions for this family. More...

HAS-barrel ATP-synt_ab_C ATP-synt_DE_N ATP-synt_ab ATP-synt_F6 ATP-synt_DE vATP-synt_E ATP-synt_DE_N ATP-synt_ab OSCP Mt_ATP-synt_B HAS-barrel ATP-synt_ab_N ATP-synt ATP-synt ATP-synt_ab_C


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 496 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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