Summary: Signal peptidase subunit
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This is the Wikipedia entry entitled "Signal peptidase". More...
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Signal peptidase Edit Wikipedia article
Initially observed in preparations of Endoplasmci reticulum (ER)-derived membranes, so called "microsomes" from mouse myeloma cells , 'signal peptidase convert secretory and some membrane proteins to their mature form. The key observation by Milstein et al. was that immunoglobulin light chains were produced in a higher molecular weight form, which became processed by the microsomal fraction. This finding was directly followed by the discovery of the ER translocation machinery . Signal peptidases are also found in prokaryotes as well as the protein import machinery of mitochondria and chloroplasts .
All signal peptidases described so far are serine proteases. The active site that endoproteolytically cleaves signal peptides from translocated precursor proteins is located at the extracytoplasmic site of the membrane. The eukaryotic signal peptidase is an integral membrane protein complex. The first subunit, which was identified genetically, is Sec11, yeast membrane protein of 17 kDa. Sec11 is associated with three subunits termed Spc3p (21 kDa), Spc2p (18 kDa) and Spc1p (11 kDa). Sec11 is the only essential factor for signal peptide processing as can be deduced from a growth defect upon its deletion . The functional signal peptidase complex was first purified from canine microsomes . The five mammalian subunits are named SPC12, SPC18, SPC21, SPC22/23 and SPC25 according to their molecular weight.
- Milstein, C., Brownlee, G. G., Harrison, T. M., and Mathews, M. B. (1972). A possible precursor of immunoglobulin light chains. Nat New Biol 239, PP. 117-120
- Blobel, G., and Dobberstein, B. (1975). Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J Cell Biol 67, PP. 835-851
- Paetzel, M., Karla, A., Strynadka, N. C., and Dalbey, R. E. (2002b). Signal peptidases. Chem Rev 102, PP. 4549-4580
- Bohni, P. C., Deshaies, R. J., and Schekman, R. W. (1988). SEC11 is required for signal peptide processing and yeast cell growth. J Cell Biol 106, PP. 1035-1042
- Evans, E. A., Gilmore, R., and Blobel, G. (1986). Purification of microsomal signal peptidase as a complex. Proc Natl Acad Sci U S A 83, PP. 581-585
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Signal peptidase subunit Provide feedback
Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals. This family is common to yeast and mammals [1,2].
This tab holds annotation information from the InterPro database.
InterPro entry IPR007653
This entry includes signal peptidase complex subunit 3 (Spc3, also known as SPC22) and its homologues from fungi, plants and animals.
Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals [ PUBMED:8632014 , PUBMED:9148931 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||integral component of membrane (GO:0016021)|
|signal peptidase complex (GO:0005787)|
|Biological process||signal peptide processing (GO:0006465)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. 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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Seed source:||Pfam-B_4675 (release 7.5)|
|Author:||Waterfield DI , Finn RD|
|Number in seed:||93|
|Number in full:||2176|
|Average length of the domain:||140.7 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||83.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|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....
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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.
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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.
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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.
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The tree shows the occurrence of this domain across different species. More...
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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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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.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.
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