Summary: Mitochondrial ATP synthase coupling factor 6

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ATP5J Edit Wikipedia article

ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6

Identifiers

Symbols

ATP5J; ATP5; ATP5A; ATPM; CF6; F6

External IDs

OMIM: 603152 MGI: 107777 HomoloGene: 1272 GeneCards: ATP5J Gene

EC number

3.6.1.14

Gene Ontology
Molecular function	• transporter activity • hydrogen ion transmembrane transporter activity • ATPase activity • transmembrane transporter activity
Cellular component	• mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) • mitochondrion • mitochondrion • mitochondrial inner membrane • mitochondrial proton-transporting ATP synthase complex • membrane
Biological process	• ATP catabolic process • transport • ion transport • respiratory electron transport chain • mitochondrial ATP synthesis coupled proton transport • mitochondrial ATP synthesis coupled proton transport • small molecule metabolic process
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 21:
27.09 – 27.11 Mb

Chr 16:
84.83 – 84.84 Mb

PubMed search

[1]

[2]

Mitochondrial ATP synthase coupling factor 6 (F6)

solution structure of subunit f6 from the peripheral stalk region of atp synthase from bovine heart mitochondria

Identifiers

Symbol

ATP-synt_F6

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

ATP synthase-coupling factor 6, mitochondrial is an enzyme that in humans is encoded by the ATP5J gene.^[1]^[2]^[3]

Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, F0, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The F0 seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the F6 subunit of the F0 complex, required for F1 and F0 interactions. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene.^[3]

The F6 subunit is part of the peripheral stalk that links the F1 and FO complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D.^[4] There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria.

[edit] References

^ Higuti T, Tsurumi C, Kawamura Y, Tsujita H, Osaka F, Yoshihara Y, Tani I, Tanaka K, Ichihara A (Aug 1991). "Molecular cloning of cDNA for the import precursor of human coupling factor 6 of H(+)-ATP synthase in mitochondria". Biochem Biophys Res Commun 178 (2): 793–9. doi:10.1016/0006-291X(91)90178-A. PMID 1830479.
^ Javed AA, Ogata K, Sanadi DR (Apr 1991). "Human mitochondrial ATP synthase: cloning cDNA for the nuclear-encoded precursor of coupling factor 6". Gene 97 (2): 307–10. doi:10.1016/0378-1119(91)90068-M. PMID 1825642.
^ ^a ^b "Entrez Gene: ATP5J ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=522.
^ Carbajo RJ, Kellas FA, Runswick MJ, Montgomery MG, Walker JE, Neuhaus D (August 2005). "Structure of the F1-binding domain of the stator of bovine F1Fo-ATPase and how it binds an alpha-subunit". J. Mol. Biol. 351 (4): 824–38. doi:10.1016/j.jmb.2005.06.012. PMID 16045926.

[edit] Further reading

Kinosita K, Yasuda R, Noji H (2003). "F1-ATPase: a highly efficient rotary ATP machine.". Essays Biochem. 35: 3–18. PMID 12471886.
Oster G, Wang H (2003). "Rotary protein motors.". Trends Cell Biol. 13 (3): 114–21. doi:10.1016/S0962-8924(03)00004-7. PMID 12628343.
Leyva JA, Bianchet MA, Amzel LM (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.
Hochstrasser DF, Frutiger S, Paquet N, et al. (1993). "Human liver protein map: a reference database established by microsequencing and gel comparison.". Electrophoresis 13 (12): 992–1001. doi:10.1002/elps.11501301201. PMID 1286669.
Yan WL, Lerner TJ, Haines JL, Gusella JF (1995). "Sequence analysis and mapping of a novel human mitochondrial ATP synthase subunit 9 cDNA (ATP5G3).". Genomics 24 (2): 375–7. doi:10.1006/geno.1994.1631. PMID 7698763.
Elston T, Wang H, Oster G (1998). "Energy transduction in ATP synthase.". Nature 391 (6666): 510–3. doi:10.1038/35185. PMID 9461222.
Webster KA, Oliver NA, Wallace DC (1998). "Assignment of an oligomycin-resistance locus to human chromosome 10.". Somatic Cell Genet. 8 (2): 223–44. doi:10.1007/BF01538679. PMID 9732751.
Wang H, Oster G (1998). "Energy transduction in the F1 motor of ATP synthase.". Nature 396 (6708): 279–82. doi:10.1038/24409. PMID 9834036.
Hattori M, Fujiyama A, Taylor TD, et al. (2000). "The DNA sequence of human chromosome 21.". Nature 405 (6784): 311–9. doi:10.1038/35012518. PMID 10830953.
Wiemann S, Weil B, Wellenreuther R, et al. (2001). "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs.". Genome Res. 11 (3): 422–35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=311072.
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): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.
Osanai T, Nakamura M, Sasaki S, et al. (2004). "Plasma concentration of coupling factor 6 and cardiovascular events in patients with end-stage renal disease.". Kidney Int. 64 (6): 2291–7. doi:10.1046/j.1523-1755.2003.00334.x. PMID 14633154.
Cross RL (2004). "Molecular motors: turning the ATP motor.". Nature 427 (6973): 407–8. doi:10.1038/427407b. PMID 14749816.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=528928.
Jacobs LJ, de Coo IF, Nijland JG, et al. (2005). "Transmission and prenatal diagnosis of the T9176C mitochondrial DNA mutation.". Mol. Hum. Reprod. 11 (3): 223–8. doi:10.1093/molehr/gah152. PMID 15709156.

This article incorporates text from the public domain Pfam and InterPro IPR008387

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Mitochondrial ATP synthase coupling factor 6 Provide feedback

Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments [1].

Literature references

Javed AA, Ogata K, Sanadi DR; , Gene 1991;97:307-310.: Human mitochondrial ATP synthase: cloning cDNA for the nuclear-encoded precursor of coupling factor 6. PUBMED:1825642 EPMC:1825642

External database links

PANDIT:	PF05511
Pseudofam:	PF05511
SYSTERS:	ATP-synt_F6

This tab holds annotation information from the InterPro database.

InterPro entry IPR008387

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.

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 to hydrolyse ATP to create a proton gradient.

This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D [PUBMED:16045926]. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria.

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	mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)
Molecular function	hydrogen ion transmembrane transporter activity (GO:0015078)
Biological process	ATP synthesis coupled proton transport (GO:0015986)

Domain organisation

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Alignments

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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meta: alignment generated by searching the metagenomics sequence database using the family HMM

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	Seed (17)	Full (159)	Representative proteomes				NCBI (157)	Meta (0)
	Seed (17)	Full (159)	RP15 (25)	RP35 (33)	RP55 (56)	RP75 (80)	NCBI (157)	Meta (0)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (17)	Full (159)	Representative proteomes				NCBI (157)	Meta (0)
	Seed (17)	Full (159)	RP15 (25)	RP35 (33)	RP55 (56)	RP75 (80)	NCBI (157)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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 (17)	Full (159)	Representative proteomes				NCBI (157)	Meta (0)
	Seed (17)	Full (159)	RP15 (25)	RP35 (33)	RP55 (56)	RP75 (80)	NCBI (157)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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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.

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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.

Curation

Seed source:

Pfam-B_9347 (release 8.0)

Previous IDs:

none

Type:

Family

Author:

Moxon SJ

Number in seed:

17

Number in full:

159

Average length of the domain:

92.10 aa

Average identity of full alignment:

42 %

Average coverage of the sequence by the domain:

71.49 %

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	27.9	27.9
Trusted cut-off	28.5	31.6
Noise cut-off	27.7	27.8

Model length:

99

Family (HMM) version:

6

Download:

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Species distribution

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Interactive tree

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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_F6 domain has been found. There are 5 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: ATP-synt_F6 (PF05511)

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