Summary: Signal peptidase (SPase) II
Signal peptidase (SPase) II Provide feedback
No Pfam abstract.
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This tab holds annotation information from the InterPro database.
InterPro entry IPR001872
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
Aspartic endopeptidases EC of vertebrate, fungal and retroviral origin have been characterised [PUBMED:1455179]. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [PUBMED:10625704] and archaean preflagellin have been described [PUBMED:16983194, PUBMED:14622420].
Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.
This group of aspartic peptidases belong to the MEROPS peptidase family A8 (signal peptidase II family, clan AC). The catalytic residues have not been identified, but three conserved aspartates can be identified from sequence alignments. The type example is the Escherichia coli lipoprotein signal peptidase or SPase II (EC). This enzyme recognises a conserved sequence and cuts in front of a cysteine residue to which a glyceride-fatty acid lipid is attached. SPase II is an integral membrane protein that is anchored in the membrane.
Bacterial cell walls contain large amounts of murein lipoprotein, a small protein that is both N-terminally bound to lipid and attached to membrane peptidoglycan (murein) through the epsilon-amino group of its C-terminal lysine residue [PUBMED:7674916]. Secretion of this lipoprotein is facilitated by the action of the lipoprotein signal peptidases in this entry, located in the inner membrane [PUBMED:7674916, PUBMED:6368552]. They enzyme are inhibited by globomycin and also by pepstatin, suggesting that they are aspartic peptidases [PUBMED:7674916].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||aspartic-type endopeptidase activity (GO:0004190)|
|Biological process||proteolysis (GO:0006508)|
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This example describes an architecture with one
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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Curation and family details
|Author:||Finn RD, Bateman A|
|Number in seed:||181|
|Number in full:||4771|
|Average length of the domain:||151.40 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||88.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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