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

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ATP synthase alpha/beta subunits

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

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

ATP synthase alpha/beta family, nucleotide-binding domain

Identifiers

Symbol

ATP-synt_ab

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

ATP synthase alpha/beta chain, C terminal domain

Identifiers

Symbol

ATP-synt_ab_C

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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].

[edit] Human proteins containing this domain

ATP5A1; ATP5B; ATP6V1A; ATP6V1B1; ATP6V1B2;

[edit] 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. doi:10.1016/j.febslet.2004.08.065. PMID 15473999.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1303195.

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

No Pfam abstract.

Literature references

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

External database links

HOMSTRAD:	ATP-synt
PANDIT:	PF00306
Pseudofam:	PF00306
SCOP:	1bmf
SYSTERS:	ATP-synt_ab_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR000793

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 [PUBMED:15473999, PUBMED:15078220].

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, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-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.

This entry represents the alpha and beta subunits found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively (sometimes called the A and B subunits in V- and A-ATPases). 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 is 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 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, where the central region is the nucleotide-binding domain (INTERPRO) [PUBMED:12885621]. This entry represents the C-terminal domain of the alpha/A/beta/B subunits, 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].

More information about this protein can be found at Protein of the Month: ATP Synthases [PUBMED:].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)
Molecular function	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)
Biological process	ATP hydrolysis coupled proton transport (GO:0015991)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

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Alignment:	Seed (150) Full (15483) NCBI (12920) Metagenomics (5134)
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Alignment:	Seed (150) Full (15483)
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Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (150) Full (15483) NCBI (12920) Metagenomics (5134)
Full length sequences	Full-sequences (15483)

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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:

Pfam-B_15 (release 1.0)

Previous IDs:

none

Type:

Domain

Author:

Finn RD, Griffiths-Jones SR

Number in seed:

150

Number in full:

15483

Average length of the domain:

102.40 aa

Average identity of full alignment:

35 %

Average coverage of the sequence by the domain:

21.58 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 15929002 -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	21.2	21.3

Model length:

113

Family (HMM) version:

22

Download:

download the raw HMM for this family

Species distribution

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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab if you need to select sub-trees and view sequence alignments. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, it's distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

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class
order
family
genus
species

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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

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

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

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 207 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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Family: ATP-synt_ab_C (PF00306)

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

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ATP synthase alpha/beta subunits

[edit] Human proteins containing this domain

[edit] References

ATP synthase alpha/beta chain, C terminal domain

Literature references

External database links

InterPro entry IPR000793

Gene Ontology

Domain organisation

Alignments

Viewing

Downloading

View options

Formatting options

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures