Summary: ATP synthase (F/14-kDa) subunit

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Wikipedia: ATP6V1F
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ATP6V1F Edit Wikipedia article

ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F

Identifiers

Symbols

ATP6V1F; ATP6S14; VATF; Vma7

External IDs

OMIM: 607160 MGI: 1913394 HomoloGene: 3119 GeneCards: ATP6V1F Gene

EC number

3.6.3.14

Gene Ontology
Molecular function	protein binding hydrogen ion transmembrane transporter activity ATPase activity, uncoupled hydrogen ion transporting ATP synthase activity, rotational mechanism proton-transporting ATPase activity, rotational mechanism
Cellular component	membrane fraction cytosol membrane proton-transporting two-sector ATPase complex vacuolar proton-transporting V-type ATPase complex proton-transporting V-type ATPase, V1 domain
Biological process	ion transport cellular iron ion homeostasis insulin receptor signaling pathway ATP hydrolysis coupled proton transport proton transport transferrin transport transmembrane transport
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 7:
128.5 128.51 Mb

Chr 6:
29.42 29.42 Mb

PubMed search

[1]

[2]

ATP-synt_F

Identifiers

Symbol

ATP-synt_F

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

V-type proton ATPase subunit F is an enzyme that in humans is encoded by the ATP6V1F gene.^[1]^[2]^[3]

This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is the V1 domain F subunit protein.^[3]

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.^[4]

[edit] References

^ Fujiwara T, Kawai A, Shimizu F, Hirano H, Okuno S, Takeda S, Ozaki K, Shimada Y, Nagata M, Watanabe T, et al. (Mar 1996). "Cloning, sequencing and expression of a novel cDNA encoding human vacuolar ATPase (14-kDa subunit)". DNA Res 2 (3): 10711. doi:10.1093/dnares/2.3.107. PMID 8581736.
^ Peng SB, Crider BP, Tsai SJ, Xie XS, Stone DK (Jun 1996). "Identification of a 14-kDa subunit associated with the catalytic sector of clathrin-coated vesicle H+-ATPase". J Biol Chem 271 (6): 33247. doi:10.1074/jbc.271.6.3324. PMID 8621738.
^ ^a ^b "Entrez Gene: ATP6V1F ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=9296.
^ Imamura H, Ikeda C, Yoshida M, Yokoyama K (April 2004). "The F subunit of Thermus thermophilus V1-ATPase promotes ATPase activity but is not necessary for rotation". J. Biol. Chem. 279 (17): 1808590. doi:10.1074/jbc.M314204200. PMID 14963028.

[edit] Further reading

Finbow ME, Harrison MA (1997). "The vacuolar H+-ATPase: a universal proton pump of eukaryotes". Biochem. J. 324 (3): 697712. PMC 1218484. PMID 9210392. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1218484.
Stevens TH, Forgac M (1998). "Structure, function and regulation of the vacuolar (H+)-ATPase". Annu. Rev. Cell Dev. Biol. 13: 779808. doi:10.1146/annurev.cellbio.13.1.779. PMID 9442887.
Nelson N, Harvey WR (1999). "Vacuolar and plasma membrane proton-adenosinetriphosphatases". Physiol. Rev. 79 (2): 36185. PMID 10221984.
Forgac M (1999). "Structure and properties of the vacuolar (H+)-ATPases". J. Biol. Chem. 274 (19): 129514. doi:10.1074/jbc.274.19.12951. PMID 10224039.
Kane PM (1999). "Introduction: V-ATPases 1992-1998". J. Bioenerg. Biomembr. 31 (1): 35. doi:10.1023/A:1001884227654. PMID 10340843.
Wieczorek H, Brown D, Grinstein S, et al. (1999). "Animal plasma membrane energization by proton-motive V-ATPases". Bioessays 21 (8): 63748. doi:10.1002/(SICI)1521-1878(199908)21:8<637::AID-BIES3>3.0.CO;2-W. PMID 10440860.
Nishi T, Forgac M (2002). "The vacuolar (H+)-ATPases--nature's most versatile proton pumps". Nat. Rev. Mol. Cell Biol. 3 (2): 94103. doi:10.1038/nrm729. PMID 11836511.
Kawasaki-Nishi S, Nishi T, Forgac M (2003). "Proton translocation driven by ATP hydrolysis in V-ATPases". FEBS Lett. 545 (1): 7685. doi:10.1016/S0014-5793(03)00396-X. PMID 12788495.
Morel N (2004). "Neurotransmitter release: the dark side of the vacuolar-H+ATPase". Biol. Cell 95 (7): 4537. doi:10.1016/S0248-4900(03)00075-3. PMID 14597263.
Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. 6 (3): 23644. doi:10.1038/ng0394-236. PMID 8012384.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.

This article incorporates text from the public domain Pfam and InterPro IPR008218

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ATP synthase (F/14-kDa) subunit Provide feedback

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 EPMC: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 EPMC: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 EPMC:8702544

External database links

PANDIT:	PF01990
Pseudofam:	PF01990
SYSTERS:	ATP-synt_F

This tab holds annotation information from the InterPro database.

InterPro entry IPR008218

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 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

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	proton-transporting ATPase activity, rotational mechanism (GO:0046961)
Molecular function	hydrogen ion transporting ATP synthase activity, rotational mechanism (GO:0046933)
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

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (100)	Full (1179)	Representative proteomes				NCBI (861)	Meta (109)
	Seed (100)	Full (1179)	RP15 (171)	RP35 (280)	RP55 (387)	RP75 (454)	NCBI (861)	Meta (109)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (100)	Full (1179)	Representative proteomes				NCBI (861)	Meta (109)
	Seed (100)	Full (1179)	RP15 (171)	RP35 (280)	RP55 (387)	RP75 (454)	NCBI (861)	Meta (109)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (100)	Full (1179)	Representative proteomes				NCBI (861)	Meta (109)
	Seed (100)	Full (1179)	RP15 (171)	RP35 (280)	RP55 (387)	RP75 (454)	NCBI (861)	Meta (109)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

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

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.

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'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.

Note: You can also download the data file for the tree.

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:

100

Number in full:

1179

Average length of the domain:

94.90 aa

Average identity of full alignment:

28 %

Average coverage of the sequence by the domain:

86.32 %

HMM information

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	23.5	23.5
Trusted cut-off	23.5	23.5
Noise cut-off	23.4	23.2

Model length:

95

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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. 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

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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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kingdom
phylum
class
order
family
genus
species

Colouring and labels

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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

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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 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 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_F domain has been found. There are 17 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: ATP-synt_F (PF01990)

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Summary: ATP synthase (F/14-kDa) subunit

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ATP6V1F Edit Wikipedia article

[edit] References

[edit] Further reading

ATP synthase (F/14-kDa) subunit Provide feedback

Literature references

External database links

InterPro entry IPR008218

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

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

Selections

Currently selected:

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

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Selected sequences

Species trees

Interactive tree

Interactions

Structures