Summary: E1-E2 ATPase
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Proton ATPase Edit Wikipedia article
- ATP + H
2O + H+
in ADP + phosphate + H+
Proton ATPases are divided into three groups as outlined below:
P-type proton ATPase
P-type ATPases form a covalent phosphorylated (hence the symbol â€™P') intermediate as part of its reaction cycle. P-type ATPases undergo major conformational changes during the catalytic cycle. P-type ATPases are not evolutionary related to V- and F-type ATPases.
Plasma membrane H+-ATPase
P-type proton ATPase (or plasma membrane H+
-ATPase) is found in the plasma membranes of eubacteria, archaea, protozoa, fungi and plants. Here it serves as a functional equivalent to the Na+/K+ ATPase of animal cells; i.e. it energizes the plasma membrane by forming an electrochemical gradient of protons (Na+ in animal cells), that in turn drives secondary active transport processes across the membrane. The plasma membrane H+-ATPase is a P3A ATPase with a single polypeptide of 70-100 kDa.
Gastric H+/K+ ATPase
Animals have a gastric hydrogen potassium ATPase or H+/K+ ATPase that belongs to the P-type ATPase family and functions as an electroneutral proton pump. This pump is found in the plasma membrane of cells in the gastric mucosa and functions to acidify the stomach. This enzyme is a P2C ATPase, characterized by having a supporting beta-subunit, and is closely related to the Na+/K+ ATPase.
V-type proton ATPase
V-type proton ATPase (or V-ATPase) translocate protons into intracellular organelles other than mitochondria and chloroplasts, but in certain cell types they are also found in the plasma membrane. V-type ATPases acidify the lumen of the vacuole (hence the symbol 'V') of fungi and plants, and that of the lysosome in animal cells. Furthermore, they are found in endosomes, clathrin coated vesicles, hormone storage granules, secretory granules, Golgi vesicles and in the plasma membrane of a variety of animal cells. Like F-type ATPases, V-type ATPases are composed of multiple subunits and carry out rotary catalysis. The reaction cycle involves tight binding of ATP but proceeds without formation of a covalent phosphorylated intermediate. V-type ATPases are evolutionary related to F-type ATPases.
F-type proton ATPase
F-type proton ATPase (or F-ATPase) typically operates as an ATP synthase that dissipates a proton gradient rather than generating one; i.e. protons flow in the reverse direction compared to V-type ATPases. In eubacteria, F-type ATPases are found in plasma membranes. In eukaryotes, they are found in the mitochondrial inner membranes and in chloroplast thylakoid membranes. Like V-type ATPases, F-type ATPases are composed of multiple subunits and carry out rotary catalysis. The reaction cycle involves tight binding of ATP but proceeds without formation of a covalent phosphorylated intermediate. F-type ATPases are evolutionary related to V-type ATPases.
- Pedersen PL, Carafoli E (1987). "Ion motive ATPases. I. Ubiquity, properties, and significance to cell function". Trends in Biochemical Sciences. 12: 146â€“50. doi:10.1016/0968-0004(87)90071-5.
- Goffeau A, Slayman CW (December 1981). "The proton-translocating ATPase of the fungal plasma membrane". Biochimica et Biophysica Acta. 639 (3â€“4): 197â€“223. doi:10.1016/0304-4173(81)90010-0. PMID 6461354.
- Morsomme P, Slayman CW, Goffeau A (November 2000). "Mutagenic study of the structure, function and biogenesis of the yeast plasma membrane H(+)-ATPase". Biochimica et Biophysica Acta. 1469 (3): 133â€“57. doi:10.1016/S0304-4157(00)00015-0. PMID 11063881.
- Palmgren MG (June 2001). "PLANT PLASMA MEMBRANE H+-ATPases: Powerhouses for Nutrient Uptake". Annual Review of Plant Physiology and Plant Molecular Biology. 52: 817â€“845. doi:10.1146/annurev.arplant.52.1.817. PMID 11337417.
- Morth JP, Pedersen BP, Buch-Pedersen MJ, Andersen JP, Vilsen B, Palmgren MG, Nissen P (January 2011). "A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps". Nature Reviews. Molecular Cell Biology. 12 (1): 60â€“70. doi:10.1038/nrm3031. PMID 21179061.
- Sachs G, Shin JM, Briving C, Wallmark B, Hersey S (1995). "The pharmacology of the gastric acid pump: the H+,K+ ATPase". Annu Rev Pharmacol Toxicol. 35: 277â€“305. doi:10.1146/annurev.pa.35.040195.001425. PMID 7598495.
- Beyenbach KW, Wieczorek H (February 2006). "The V-type H+ ATPase: molecular structure and function, physiological roles and regulation". The Journal of Experimental Biology. 209 (Pt 4): 577â€“89. doi:10.1242/jeb.02014. PMID 16449553.
- Nelson N (November 1992). "The vacuolar H(+)-ATPase--one of the most fundamental ion pumps in nature". The Journal of Experimental Biology. 172: 19â€“27. PMID 1337091.
- Marshansky V, Rubinstein JL, GrÃ¼ber G (June 2014). "Eukaryotic V-ATPase: novel structural findings and functional insights". Biochimica et Biophysica Acta. 1837 (6): 857â€“79. doi:10.1016/j.bbabio.2014.01.018. PMID 24508215.
- Stewart AG, Laming EM, Sobti M, Stock D (April 2014). "Rotary ATPases--dynamic molecular machines". Current Opinion in Structural Biology. 25: 40â€“8. doi:10.1016/j.sbi.2013.11.013. PMID 24878343.
- Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV (November 2007). "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases". Nature Reviews. Microbiology. 5 (11): 892â€“9. doi:10.1038/nrmicro1767. PMID 17938630.
- Boyer PD (1997). "The ATP synthase--a splendid molecular machine". Annual Review of Biochemistry. 66: 717â€“49. doi:10.1146/annurev.biochem.66.1.717. PMID 9242922.
- Junge W, Nelson N (2015). "ATP synthase". Annual Review of Biochemistry. 84: 631â€“57. doi:10.1146/annurev-biochem-060614-034124. PMID 25839341.
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.
E1-E2 ATPase Provide feedback
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|PRINTS:||PR00119 PR00120 PR00121|
This tab holds annotation information from the InterPro database.
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Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
|Author:||Sonnhammer ELL , Bateman A|
|Number in seed:||74|
|Number in full:||67430|
|Average length of the domain:||186.60 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||21.14 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||21|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
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.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
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.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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There are 9 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 E1-E2_ATPase domain has been found. There are 198 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 sequence.
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