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406  structures 11148  species 4  interactions 20853  sequences 34  architectures

Family: ATP-synt_ab_C (PF00306)

Summary: ATP synthase alpha/beta chain, C terminal 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
Identifiers
Symbol ATP-synt_ab_N
Pfam PF02874
InterPro IPR004100
PROSITE PDOC00137
SCOP 1bmf
SUPERFAMILY 1bmf
ATP synthase alpha/beta family, nucleotide-binding domain
Identifiers
Symbol ATP-synt_ab
Pfam PF00006
InterPro IPR000194
PROSITE PDOC00137
SCOP 1bmf
SUPERFAMILY 1bmf
ATP synthase alpha/beta chain, C terminal domain
Identifiers
Symbol ATP-synt_ab_C
Pfam PF00306
InterPro IPR000793
SCOP 1bmf
SUPERFAMILY 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 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[edit]

ATP5A1; ATP5B; ATP6V1A; ATP6V1B1; ATP6V1B2;

References[edit]

  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.

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

No Pfam abstract.

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


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 (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 eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles.
  • 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).
  • 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 C-terminal domain, which forms a left-handed superhelix composed of 4-5 individual helices. The C-terminal domain can vary between the alpha and beta subunits, and between different ATPases [PUBMED:11309608].

Gene Ontology

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Domain organisation

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  Seed
(150)
Full
(20853)
Representative proteomes NCBI
(16060)
Meta
(5135)
RP15
(1226)
RP35
(2225)
RP55
(2960)
RP75
(3509)
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  Seed
(150)
Full
(20853)
Representative proteomes NCBI
(16060)
Meta
(5135)
RP15
(1226)
RP35
(2225)
RP55
(2960)
RP75
(3509)
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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_15 (release 1.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 150
Number in full: 20853
Average length of the domain: 103.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 21.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 113
Family (HMM) version: 22
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Interactions

There are 4 interactions for this family. More...

ATP-synt ATP-synt_ab_N ATP-synt_ab ATP-synt_ab_C

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 406 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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