ATP Synthase

What InterPro Tells Us

P10719 Rat mitochondrial F-ATP synthase, beta chain

InterPro Domain Architecture

InterPro Entry	Signatures	Graphical Match	Method Name
IPR000194	PF00006		ATP-synt_ab
IPR000194	PS00152		ATPASE_ALPHA_BETA
IPR000793	PF00306		ATP-synt_ab_C
IPR000793	SSF47917		ATPase_a/b_C
IPR003593	SM00382		AAA
IPR004100	PF02874		ATP-synt_ab_N
IPR004100	SSF50615		ATPase_a/b_N
IPR005722	PTHR15184:SF4		ATP_synthF1_beta
IPR005722	TIGR01039		atpD
Structural Features
1mab	1mabB
1.10.1140.10.1	1mabB3
2.40.10.170.1	1mabB1
3.40.50.300.68	1mabB2
a.69.1.1	d1mabb1
b.49.1.1	d1mabb2
c.37.1.11	d1mabb3

From the graphical match above, you can see that the signatures are grouped into five InterPro entries for the beta subunit of rat mitochondrial F-ATP synthase. These entries give information about the domain architecture of the protein, as well as its family relationships.

To look at the family relationships, we need to consider entry IPR005722, which represents the family of F-ATP synthase b subunits, and which has two signatures, PTHR15184:SF4 from the PANTHER database, and TIGR01039 from the TIGRFAMs database. In InterPro, each ATPase subunit has been classified into a different entry, with its own unique signatures.

The domain architecture of the beta subunit of rat F-ATP synthase consists of three domains: the N-terminal beta-barrel domain, a central nucleotide-binding domain, and a C-terminal alpha-helical domain. IPR004100 represents the N-terminal beta-barrel domain found in both the alpha and beta subunits of several types of ATPases, and is represented by two signatures, PF02874 from the PFAM database and SSF50615 from the SUPERFAMILY database. If you follow the links to this entry, you will find many entries under the section labelled ‘Found in’, which represents the list of ATPases that contain this domain. IPR000194 represents the central nucleotide-binding domain found in both the alpha and beta subunits of several types of ATPases (a list is given in the ‘Found in’ section), and which is represented by two signatures: PF00006 from the PFAM database, and PS00152 from the PROSITE database, the latter covering a 10-residue motif containing two conserved serines, one being important for catalysis. This domain is also represented by IPR003593, which corresponds to the larger class of AAA-ATPases, a large functionally diverse family of ring-shaped P-loop-containing NTPases that share a common structure. As such, the AAA-ATPase-type domain is ‘Found in’ a wide number of protein families besides F-ATPase. IPR003593 has one signature, SM00382 from the SMART database. The remaining domain is covered by IPR000793, which represents the C-terminal alpha-helical domain found in both the alpha and beta subunits of several types of ATPases, and which is represented by two signatures, PF00306 from the PFAM database, and SSF47917 from the SUPERFAMILY database.

The remaining seven entries in the table above give information on the structure of this protein, presenting known structural data from the structural database PDB (green stripe) and the structural classification databases CATH (pink stripe) and SCOP (black stripe) (the names such as d1mabb1 are derived from the PDB entry upon which they are based, here PDB entry 1mab, chain B, fragment 1). The graphical match for the PDB entry 1mabB displays the full length of the original PDB entry, here covering almost the entire length of the protein. The CATH and SCOP entries breakdown the PDB data into the three constituent domains and provide a structural classification of each: the N-terminal beta-barrel domain (1mabB1 and d1mabb2), the central nucleotide-binding domain (1mabB2 and d1mabb3), and the C-terminal alpha-helical domain (1mabB3 and d1mabb1).

What the Structure Tells Us

Structures associated with the beta subunit of rat mitochondrial F-ATP synthase can be viewed using AstexViewer®, which is linked from the Match Table via the logo on the InterPro page (please note, there is no link directly from this page to the AstexViewer®, therefore you need to go to the link on the InterPro page for P10719). The AstexViewer® displays the PDB structure with the CATH or SCOP domain highlighted.

There are structures available for various ATP synthases from several different species in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of ATP synthase can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of different subunits of ATP synthases have provided insight into the rotational mechanism of action of these important enzymes, and how these enzymes use their rotational motors to drive ATP synthesis.

Next: Table of ATP Synthase Proteins

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