Summary: ATP synthase delta (OSCP) subunit

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Wikipedia: ATP synthase delta subunit
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ATP synthase delta subunit Edit Wikipedia article

ATP synthase delta (OSCP) subunit

Structure of the N-terminal domain of the delta subunit of the E. coli ATPsynthase.^[1]

Identifiers

Symbol

OSCP

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

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.

[edit] References

^ 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.
^ 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.

[edit] Further reading

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

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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

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

PANDIT:	PF00213
PRINTS:	PR00125
PROSITE:	PDOC00327
Pseudofam:	PF00213
SCOP:	1abv
SYSTERS:	OSCP
Transporter classification:	3.A.2

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.

Molecular function	hydrogen ion transporting ATP synthase activity, rotational mechanism (GO:0046933)
Biological process	ATP synthesis coupled proton transport (GO:0015986)

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 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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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.

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

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

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:

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Species distribution

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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.

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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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: OSCP (PF00213)

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