Summary: Fungal ATP synthase protein 8 (A6L)
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MT-ATP8 Edit Wikipedia article
|, ATPase8, MTMT-ATP synthase F0 subunit 8|
|ATP synthase protein 8 (metazoa)|
|Plant ATP synthase F0 subunit 8|
|Fungal ATP synthase protein 8 (A6L)|
ATP synthase protein 8 is a subunit of mitochondrial ATP synthase.
This protein subunit appears to be an integral component of the stator stalk in yeast mitochondrial F-ATPases. The stator stalk is anchored in the membrane, and acts to prevent futile rotation of the ATPase subunits relative to the rotor during coupled ATP synthesis/hydrolysis. This subunit may have an analogous function in Metazoa.
The ATP synthase protein 8 of human and other mammals is encoded in the mitochondrial genome by the MT-ATP8 gene. When the complete human mitochondrial genome was first published, the MT-ATP8 gene was described as the unidentified reading frame URF A6L.
An unusual feature of the MT-ATP8 gene is its 46-nucleotide overlap with the MT-ATP6 gene. With respect to the reading frame (+1) of MT-ATP8, the MT-ATP6 gene starts on the +3 reading frame.
- "Human PubMed Reference:".
- Stephens AN, Khan MA, Roucou X, Nagley P, Devenish RJ (May 2003). "The molecular neighborhood of subunit 8 of yeast mitochondrial F1F0-ATP synthase probed by cysteine scanning mutagenesis and chemical modification". J. Biol. Chem. 278 (20): 17867–75. doi:10.1074/jbc.M300967200. PMID 12626501.
- Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (April 1981). "Sequence and organization of the human mitochondrial genome". Nature. 290 (5806): 457–65. doi:10.1038/290457a0. PMID 7219534.
- Torroni A, Achilli A, Macaulay V, et al. (2006). "Harvesting the fruit of the human mtDNA tree.". Trends Genet. 22 (6): 339–45. doi:10.1016/j.tig.2006.04.001. PMID 16678300.
- Bodenteich A, Mitchell LG, Polymeropoulos MH, Merril CR (1993). "Dinucleotide repeat in the human mitochondrial D-loop.". Hum. Mol. Genet. 1 (2): 140. doi:10.1093/hmg/1.2.140-a. PMID 1301157.
- Lu X, Walker T, MacManus JP, Seligy VL (1992). "Differentiation of HT-29 human colonic adenocarcinoma cells correlates with increased expression of mitochondrial RNA: effects of trehalose on cell growth and maturation.". Cancer Res. 52 (13): 3718–25. PMID 1377597.
- Marzuki S, Noer AS, Lertrit P, et al. (1992). "Normal variants of human mitochondrial DNA and translation products: the building of a reference data base.". Hum. Genet. 88 (2): 139–45. doi:10.1007/bf00206061. PMID 1757091.
- Moraes CT, Andreetta F, Bonilla E, et al. (1991). "Replication-competent human mitochondrial DNA lacking the heavy-strand promoter region.". Mol. Cell. Biol. 11 (3): 1631–7. PMC . PMID 1996112.
- Attardi G, Chomyn A, Doolittle RF, et al. (1987). "Seven unidentified reading frames of human mitochondrial DNA encode subunits of the respiratory chain NADH dehydrogenase.". Cold Spring Harb. Symp. Quant. Biol. 51 (1): 103–14. doi:10.1101/sqb.1986.051.01.013. PMID 3472707.
- Chomyn A, Cleeter MW, Ragan CI, et al. (1986). "URF6, last unidentified reading frame of human mtDNA, codes for an NADH dehydrogenase subunit.". Science. 234 (4776): 614–8. doi:10.1126/science.3764430. PMID 3764430.
- Chomyn A, Mariottini P, Cleeter MW, et al. (1985). "Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase.". Nature. 314 (6012): 592–7. doi:10.1038/314592a0. PMID 3921850.
- Anderson S, Bankier AT, Barrell BG, et al. (1981). "Sequence and organization of the human mitochondrial genome.". Nature. 290 (5806): 457–65. doi:10.1038/290457a0. PMID 7219534.
- Montoya J, Ojala D, Attardi G (1981). "Distinctive features of the 5'-terminal sequences of the human mitochondrial mRNAs.". Nature. 290 (5806): 465–70. doi:10.1038/290465a0. PMID 7219535.
- Horai S, Hayasaka K, Kondo R, et al. (1995). "Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.". Proc. Natl. Acad. Sci. U.S.A. 92 (2): 532–6. doi:10.1073/pnas.92.2.532. PMC . PMID 7530363.
- Rieder MJ, Taylor SL, Tobe VO, Nickerson DA (1998). "Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome.". Nucleic Acids Res. 26 (4): 967–73. doi:10.1093/nar/26.4.967. PMC . PMID 9461455.
- Andrews RM, Kubacka I, Chinnery PF, et al. (1999). "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.". Nat. Genet. 23 (2): 147. doi:10.1038/13779. PMID 10508508.
- Ingman M, Kaessmann H, Pääbo S, Gyllensten U (2001). "Mitochondrial genome variation and the origin of modern humans.". Nature. 408 (6813): 708–13. doi:10.1038/35047064. PMID 11130070.
- Finnilä S, Lehtonen MS, Majamaa K (2001). "Phylogenetic network for European mtDNA.". Am. J. Hum. Genet. 68 (6): 1475–84. doi:10.1086/320591. PMC . PMID 11349229.
- Maca-Meyer N, González AM, Larruga JM, et al. (2003). "Major genomic mitochondrial lineages delineate early human expansions.". BMC Genet. 2: 13. doi:10.1186/1471-2156-2-13. PMC . PMID 11553319.
- Herrnstadt C, Elson JL, Fahy E, et al. (2002). "Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups.". Am. J. Hum. Genet. 70 (5): 1152–71. doi:10.1086/339933. PMC . PMID 11938495.
- Silva WA, Bonatto SL, Holanda AJ, et al. (2002). "Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America.". Am. J. Hum. Genet. 71 (1): 187–92. doi:10.1086/341358. PMC . PMID 12022039.
- Mishmar D, Ruiz-Pesini E, Golik P, et al. (2003). "Natural selection shaped regional mtDNA variation in humans.". Proc. Natl. Acad. Sci. U.S.A. 100 (1): 171–6. doi:10.1073/pnas.0136972100. PMC . PMID 12509511.
- Ingman M, Gyllensten U (2003). "Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines.". Genome Res. 13 (7): 1600–6. doi:10.1101/gr.686603. PMC . PMID 12840039.
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Fungal ATP synthase protein 8 (A6L) Provide feedback
This family consists of fungus specific ATP synthase protein 8 ( EC:22.214.171.124). The family may be related to the ATP synthase protein 8 found in other eukaryotes PF00895.
Macreadie IG, Novitski CE, Maxwell RJ, John U, Ooi BG, McMullen GL, Lukins HB, Linnane AW, Nagley P; , Nucleic Acids Res 1983;11:4435-4451.: Biogenesis of mitochondria: the mitochondrial gene (aap1) coding for mitochondrial ATPase subunit 8 in Saccharomyces cerevisiae. PUBMED:6223276 EPMC:6223276
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR009230
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 (ATP synthases, 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 eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [PUBMED:20450191]. They are also found in bacteria [PUBMED:9741106].
- 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 [PUBMED:18937357, PUBMED:1385979].
- 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 ATP synthases, 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), with additional subunits in mitochondria. 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 in bacteria, hydrolysing ATP to create a proton gradient.
In yeast, the F0 complex is composed of at least nine polypeptides which are nucleus-encoded: b, OSCP, d, e, f, g, h, i/j and k, together with three subunits, 6, 8 and 9, which are mitochondrion-encoded. The bovine enzyme also includes subunit F6 for which no homologue has been found in yeast [PUBMED:10838056].
This entry represents subunit 8 found in the F0 complex of mitochondrial F-ATPases from fungi. This subunit appears to be an integral component of the stator stalk in yeast mitochondrial F-ATPases [PUBMED:12626501]. The stator stalk is anchored in the membrane, and acts to prevent futile rotation of the ATPase subunits relative to the rotor during coupled ATP synthesis/hydrolysis. This subunit differs in sequence between fungi, Metazoa (INTERPRO) and plants (INTERPRO).
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)|
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This clan contains subunits of the F0 complex of ATP-synthase. The F0 complex is the non-catalytic unit of ATPase and is involved in proton translocation across membranes.
The clan contains the following 13 members:ATP-synt_8 ATP-synt_B FliH Fun_ATP-synt_8 HrpE Mt_ATP-synt_B NolV OSCP V-ATPase_G V-ATPase_G_2 vATP-synt_E Yae1_N YMF19
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Key: available, not generated, — not available.
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|Seed source:||Pfam-B_2993 (release 9.0)|
|Number in seed:||7|
|Number in full:||88|
|Average length of the domain:||47.90 aa|
|Average identity of full alignment:||54 %|
|Average coverage of the sequence by the domain:||53.64 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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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.
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The tree shows the occurrence of this domain across different species. More...
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