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6  structures 4570  species 0  interactions 4976  sequences 14  architectures

Family: OSCP (PF00213)

Summary: ATP synthase delta (OSCP) subunit

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This is the Wikipedia entry entitled "ATP synthase delta subunit". More...

ATP synthase delta subunit Edit Wikipedia article

ATP synthase delta (OSCP) subunit
PDB 1abv EBI.jpg
Structure of the N-terminal domain of the delta subunit of the E. coli ATPsynthase.[1]
Identifiers
Symbol OSCP
Pfam PF00213
InterPro IPR000711
PROSITE PDOC00327
SCOP 1abv
SUPERFAMILY 1abv
TCDB 3.A.2

ATP synthase delta subunit is a subunit of bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit, IPR001469).

The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B (chloroplasts).[2]

Human delta subunit of ATP synthase is coded by gene ATP5O.

References[edit]

  1. ^ Wilkens S, Dunn SD, Chandler J, Dahlquist FW, Capaldi RA (March 1997). "Solution structure of the N-terminal domain of the delta subunit of the E. coli ATPsynthase". Nat. Struct. Biol. 4 (3): 198–201. doi:10.1038/nsb0397-198. PMID 9164460. 
  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-ATPaseand how it binds an alpha-subunit". J. Mol. Biol. 351 (4): 824–838. doi:10.1016/j.jmb.2005.06.012. PMID 16045926. 

Further reading[edit]

Wilkens, S.; Rodgers, A.; Ogilvie, I.; Capaldi, R. A. (1997). "Structure and arrangement of the delta subunit in the E. Coli ATP synthase (ECF1F0)". Biophysical chemistry 68 (1–3): 95–102. PMID 9468613.  edit

This article incorporates text from the public domain Pfam and InterPro IPR000711


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 delta (OSCP) subunit Provide feedback

The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family PF00401.

Literature references

  1. Wilkens S, Rodgers A, Ogilvie I, Capaldi RA; , Biophys Chem 1997;68:95-102.: Structure and arrangement of the delta subunit in the E. coli ATP synthase (ECF1F0). PUBMED:9468613 EPMC:9468613


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000711

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 family represents subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit, INTERPRO). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) [PUBMED:11309608, 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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Pfam Clan

This family is a member of clan ATP_synthase (CL0255), which has the following description:

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 12 members:

ATP-synt_8 ATP-synt_B FliH Fun_ATP-synt_8 HrpE Mt_ATP-synt_B NolV OSCP V-ATPase_G vATP-synt_E Yae1_N YMF19

Alignments

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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
(192)
Full
(4976)
Representative proteomes NCBI
(3297)
Meta
(2540)
RP15
(405)
RP35
(776)
RP55
(1019)
RP75
(1207)
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  Seed
(192)
Full
(4976)
Representative proteomes NCBI
(3297)
Meta
(2540)
RP15
(405)
RP35
(776)
RP55
(1019)
RP75
(1207)
Alignment:
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Sequence:
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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
(192)
Full
(4976)
Representative proteomes NCBI
(3297)
Meta
(2540)
RP15
(405)
RP35
(776)
RP55
(1019)
RP75
(1207)
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.

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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

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Seed source: Prosite
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 192
Number in full: 4976
Average length of the domain: 165.70 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 84.70 %

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 21.6 21.6
Trusted cut-off 21.7 21.6
Noise cut-off 21.5 21.5
Model length: 172
Family (HMM) version: 13
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 OSCP domain has been found. There are 6 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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