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24  structures 7364  species 0  interactions 26580  sequences 265  architectures

Family: Peptidase_M48 (PF01435)

Summary: Peptidase family M48

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Peptidase family M48 Provide feedback

Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit [1,2].

Literature references

  1. Pryor EE Jr, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME;, Science. 2013;339:1600-1604.: Structure of the integral membrane protein CAAX protease Ste24p. PUBMED:23539602 EPMC:23539602

  2. Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, von Delft F, Bullock AN, Burgess-Brown NA, Carpenter EP;, Science. 2013;339:1604-1607.: The structural basis of ZMPSTE24-dependent laminopathies. PUBMED:23539603 EPMC:23539603


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001915

This entry represents the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit [ PUBMED:23539602 , PUBMED:23539603 ].

This group of metallopeptidases belong to MEROPS peptidase family M48. Proteins with this domain are mostly described as probable protease htpX homologue ( EC ) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit.

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...

View options

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
(22)
Full
(26580)
Representative proteomes UniProt
(115914)
RP15
(3510)
RP35
(12331)
RP55
(26468)
RP75
(44712)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(22)
Full
(26580)
Representative proteomes UniProt
(115914)
RP15
(3510)
RP35
(12331)
RP55
(26468)
RP75
(44712)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(22)
Full
(26580)
Representative proteomes UniProt
(115914)
RP15
(3510)
RP35
(12331)
RP55
(26468)
RP75
(44712)
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: Swiss-Prot
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 22
Number in full: 26580
Average length of the domain: 189.10 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 50.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 187
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Selections

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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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Structures

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 Peptidase_M48 domain has been found. There are 24 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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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
A0A096RSU8 View 3D Structure Click here
A0A0R0FUN2 View 3D Structure Click here
A0A0R0IM79 View 3D Structure Click here
A0A1D6FHQ3 View 3D Structure Click here
A0A1D6GNF1 View 3D Structure Click here
A0A1D6HFY1 View 3D Structure Click here
A0A1D6IXM8 View 3D Structure Click here
A0A1D6JBB8 View 3D Structure Click here
A0A1D6LI78 View 3D Structure Click here
A0A1D6NG98 View 3D Structure Click here
A0A1D6PY38 View 3D Structure Click here
A0A1D6QMN0 View 3D Structure Click here
A0A1D8PL01 View 3D Structure Click here
A1ZAM7 View 3D Structure Click here
A4I2K0 View 3D Structure Click here
B8A019 View 3D Structure Click here
D3ZS74 View 3D Structure Click here
D4A5K6 View 3D Structure Click here
E9QBI7 View 3D Structure Click here
F1QX19 View 3D Structure Click here
I1L3I9 View 3D Structure Click here
K7KY12 View 3D Structure Click here
K7LUA5 View 3D Structure Click here
K7MUD4 View 3D Structure Click here
K7U316 View 3D Structure Click here
O53978 View 3D Structure Click here
O75844 View 3D Structure Click here
P23894 View 3D Structure Click here
P25894 View 3D Structure Click here
P36163 View 3D Structure Click here
P43674 View 3D Structure Click here
P47154 View 3D Structure Click here
P66948 View 3D Structure Click here
P95164 View 3D Structure Click here
P9WHS5 View 3D Structure Click here
Q10071 View 3D Structure Click here
Q4CSD4 View 3D Structure Click here
Q4DXY8 View 3D Structure Click here
Q54FH7 View 3D Structure Click here
Q54HN7 View 3D Structure Click here
Q54M80 View 3D Structure Click here
Q55C18 View 3D Structure Click here
Q59076 View 3D Structure Click here
Q5A663 View 3D Structure Click here
Q6EPN8 View 3D Structure Click here
Q6Z754 View 3D Structure Click here
Q7JV41 View 3D Structure Click here
Q7K172 View 3D Structure Click here
Q80W54 View 3D Structure Click here
Q8MS56 View 3D Structure Click here
Q8RX88 View 3D Structure Click here
Q94DI2 View 3D Structure Click here
Q96E52 View 3D Structure Click here
Q9D8H7 View 3D Structure Click here
Q9FLI5 View 3D Structure Click here
Q9LSC4 View 3D Structure Click here
Q9P7G4 View 3D Structure Click here
Q9XVE5 View 3D Structure Click here