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3  structures 11908  species 0  interactions 17567  sequences 12  architectures

Family: ATP-synt_A (PF00119)

Summary: ATP synthase A chain

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This is the Wikipedia entry entitled "MT-ATP6". More...

MT-ATP6 Edit Wikipedia article

ATP synthase A chain
Identifiers
Symbol ATP-synt_A
Pfam PF00119
InterPro IPR000568
PROSITE PDOC00420
SCOP 1c17
SUPERFAMILY 1c17
OPM superfamily 5
OPM protein 1c17
ATP synthase F0 subunit 6
Identifiers
Symbols ATP6; ATPase6; MTATP6
External IDs OMIM516060 MGI99927 HomoloGene5012 GeneCards: ATP6 Gene
EC number 3.6.3.14
Orthologs
Species Human Mouse
Entrez 4508 17705
Ensembl ENSG00000198899 ENSMUSG00000064357
UniProt P00846 P00848
RefSeq (mRNA) n/a n/a
RefSeq (protein) YP_003024031 NP_904333
Location (UCSC) Chr MT:
0.01 – 0.01 Mb
Chr MT:
0.01 – 0.01 Mb
PubMed search [1] [2]

ATP synthase F0 subunit 6 (or subunit/chain A) (human mitochondrial gene name ATP6) is a subunit of F0 complex of transmembrane F-type ATP synthase.[1]

Function[edit]

This subunit is a key component of the proton channel, and may play a direct role in the translocation of protons across the membrane. Catalysis in the F1 complex depends upon the rotation of the central stalk and F0 c-ring, which in turn is driven by the flux of protons through the membrane via the interface between the F0 c-ring and subunit A. The peripheral stalk links subunit A to the external surface of the F1 domain, and is thought to act as a stator to counter the tendency of subunit A and the F1alpha(3)beta(3) catalytic portion to rotate with the central rotary element.[2]

3D structure of E. coli homologue of this subunit was modelled based on electron microscopy data (chain M of PDB 1c17). It forms a transmembrane 4-α-bundle.

Clinical significance[edit]

ATP6 is a gene associated with neuropathy, ataxia, and retinitis pigmentosa.[3]

References[edit]

  1. ^ 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. 
  2. ^ Walker JE, Runswick MJ, Neuhaus D, Montgomery MG, Carbajo RJ, Kellas FA (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): 824–838. doi:10.1016/j.jmb.2005.06.012. PMID 16045926. 
  3. ^ Baracca A, Sgarbi G, Mattiazzi M, Casalena G, Pagnotta E, Valentino ML, Moggio M, Lenaz G, Carelli V, Solaini G (July 2007). "Biochemical phenotypes associated with the mitochondrial ATP6 gene mutations at nt8993". Biochim. Biophys. Acta 1767 (7): 913–9. doi:10.1016/j.bbabio.2007.05.005. PMID 17568559. 


Further reading[edit]


External links[edit]

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 A chain Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000568

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 A (or subunit 6) found in the F0 complex of F-ATPases. This subunit is a key component of the proton channel, and may play a direct role in the translocation of protons across the membrane. Catalysis in the F1 complex depends upon the rotation of the central stalk and F0 c-ring, which in turn is driven by the flux of protons through the membrane via the interface between the F0 c-ring and subunit A. The peripheral stalk links subunit A to the external surface of the F1 domain, and is thought to act as a stator to counter the tendency of subunit A and the F1 alpha(3)beta(3) catalytic portion to rotate with the central rotary element [PUBMED:16045926].

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.

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...

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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
(30)
Full
(17567)
Representative proteomes NCBI
(15216)
Meta
(2921)
RP15
(343)
RP35
(689)
RP55
(893)
RP75
(1063)
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Format an alignment

  Seed
(30)
Full
(17567)
Representative proteomes NCBI
(15216)
Meta
(2921)
RP15
(343)
RP35
(689)
RP55
(893)
RP75
(1063)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(30)
Full
(17567)
Representative proteomes NCBI
(15216)
Meta
(2921)
RP15
(343)
RP35
(689)
RP55
(893)
RP75
(1063)
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.

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Sonnhammer ELL
Number in seed: 30
Number in full: 17567
Average length of the domain: 204.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 91.02 %

HMM information View help on HMM parameters

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 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.4 21.6
Model length: 215
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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_A domain has been found. There are 3 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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