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0  structures 1470  species 0  interactions 2176  sequences 34  architectures

Family: SPC22 (PF04573)

Summary: Signal peptidase subunit

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Signal peptidase". More...

Signal peptidase Edit Wikipedia article

Initially observed in preparations of Endoplasmci reticulum (ER)-derived membranes, so called "microsomes" from mouse myeloma cells [1], '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 [2]. Signal peptidases are also found in prokaryotes as well as the protein import machinery of mitochondria and chloroplasts [3].

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 [4]. The functional signal peptidase complex was first purified from canine microsomes [5]. The five mammalian subunits are named SPC12, SPC18, SPC21, SPC22/23 and SPC25 according to their molecular weight.

  1. ^ 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
  2. ^ 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
  3. ^ Paetzel, M., Karla, A., Strynadka, N. C., and Dalbey, R. E. (2002b). Signal peptidases. Chem Rev 102, PP. 4549-4580
  4. ^ 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
  5. ^ 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

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.

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].

Literature references

  1. Kalies KU, Hartmann E; , J Biol Chem 1996;271:3925-3929.: Membrane topology of the 12- and the 25-kDa subunits of the mammalian signal peptidase complex. PUBMED:8632014 EPMC:8632014

  2. Meyer HA, Hartmann E; , J Biol Chem 1997;272:13159-13164.: The yeast SPC22/23 homolog Spc3p is essential for signal peptidase activity. PUBMED:9148931 EPMC:9148931


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 ].

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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Alignments

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 and the UniProtKB sequence database. 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.

  Seed
(93)
Full
(2176)
Representative proteomes UniProt
(3556)
RP15
(442)
RP35
(1024)
RP55
(1654)
RP75
(2237)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(93)
Full
(2176)
Representative proteomes UniProt
(3556)
RP15
(442)
RP35
(1024)
RP55
(1654)
RP75
(2237)
Alignment:
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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
(93)
Full
(2176)
Representative proteomes UniProt
(3556)
RP15
(442)
RP35
(1024)
RP55
(1654)
RP75
(2237)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

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.

Curation View help on the curation process

Seed source: Pfam-B_4675 (release 7.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.3 25.7
Noise cut-off 24.6 24.8
Model length: 172
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 adjacent tab. More...

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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.

Protein Predicted structure External Information
A0A044V8E0 View 3D Structure Click here
A0A077Z7U7 View 3D Structure Click here
A0A0D2F059 View 3D Structure Click here
A0A0K0E6L2 View 3D Structure Click here
A0A0K0J036 View 3D Structure Click here
A0A0N4U1Y6 View 3D Structure Click here
A0A0N4U1Y7 View 3D Structure Click here
A0A0R0ERQ3 View 3D Structure Click here
A0A0R0F5Y6 View 3D Structure Click here
A0A175WC70 View 3D Structure Click here
A0A1C1CW12 View 3D Structure Click here
A0A1D6IAP0 View 3D Structure Click here
A0A1D6NG98 View 3D Structure Click here
A0A1D6PY38 View 3D Structure Click here
A0A1D6QNI2 View 3D Structure Click here
A0A3P7EAE4 View 3D Structure Click here
A0A3Q0KTD9 View 3D Structure Click here
A4HWF6 View 3D Structure Click here
B0G180 View 3D Structure Click here
B4FVS2 View 3D Structure Click here
B9G505 View 3D Structure Click here
C0HK79 View 3D Structure Click here
C0HK80 View 3D Structure Click here
C0NTK8 View 3D Structure Click here
C1H0M5 View 3D Structure Click here
D3ZF12 View 3D Structure Click here
I1JRE6 View 3D Structure Click here
I1LBD9 View 3D Structure Click here
I1NC08 View 3D Structure Click here
P28687 View 3D Structure Click here
P34525 View 3D Structure Click here
P61008 View 3D Structure Click here
P61009 View 3D Structure Click here
Q10259 View 3D Structure Click here
Q12133 View 3D Structure Click here
Q3SZU5 View 3D Structure Click here
Q4CMA3 View 3D Structure Click here
Q4D7H4 View 3D Structure Click here
Q4DD27 View 3D Structure Click here
Q53YF3 View 3D Structure Click here

trRosetta 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.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;