Summary

ATP synthase (F/14-kDa) subunit

This family includes 14-kDa subunit from vATPases [1] which is in the peripheral catalytic part of the complex [2]. The family also includes archaebacterial ATP synthase subunit F [3].

Literature references

Guo Y, Kaiser K, Wieczorek H, Dow JA; , Gene 1996;172:239-243.: The Drosophila melanogaster gene vha14 encoding a 14-kDa F-subunit of the vacuolar ATPase. PUBMED:8682310
Peng SB, Crider BP, Tsai SJ, Xie XS, Stone DK; , J Biol Chem 1996;271:3324-3327.: Identification of a 14-kDa subunit associated with the catalytic sector of clathrin-coated vesicle H+-ATPase. PUBMED:8621738
Wilms R, Freiberg C, Wegerle E, Meier I, Mayer F, Muller V; , J Biol Chem 1996;271:18843-18852.: Subunit structure and organization of the genes of the A1A0 ATPase from the Archaeon Methanosarcina mazei Go1. PUBMED:8702544

InterPro entry IPR008218

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.
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 V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis PUBMED:11309608, PUBMED:15629643, PUBMED:15168615. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases.

This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis PUBMED:14963028.

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

Gene Ontology

Cellular component	proton-transporting two-sector ATPase complex, catalytic domain (GO:0033178)
Molecular function	proton-transporting ATPase activity, rotational mechanism (GO:0046961)
Molecular function	hydrogen ion transporting ATP synthase activity, rotational mechanism (GO:0046933)
Biological process	ATP synthesis coupled proton transport (GO:0015986)

External database links

PANDIT:	PF01990
SYSTERS:	ATP-synt_F

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 (101) Full (442) NCBI (465) Metagenomics (109)
Viewer:

Formatting options

Alignment:	Seed (101) Full (442)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (101) Full (442) NCBI (465) Metagenomics (109)
Full length sequences	Full-sequences (442)

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 HMMER2.

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. 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:

Enright A

Previous IDs:

none

Type:

Family

Author:

Enright A, Ouzounis C, Bateman A

Number in seed:

101

Number in full:

442

Average length of the domain:

96.60 aa

Average identity of full alignment:

28 %

Average coverage of the sequence by the domain:

84.76 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	23.5	23.5
Trusted cut-off	23.5	23.7
Noise cut-off	23.3	23.3

Model length:

96

Family (HMM) version:

10

Download:

download the raw HMM for this family

Species distribution

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The tree shows the occurrence of this domain across different species. More...

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.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

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.

You can use the tree controls to manipulate how the interactive tree is displayed:

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highlight species that are represented in the seed alignment
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Interactions

There is 1 interaction for this family. More...

ATP-synt_F

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 MSD 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_F domain has been found.

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Family: ATP-synt_F (PF01990)

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