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4  structures 7218  species 0  interactions 20054  sequences 106  architectures

Family: CPBP (PF02517)

Summary: CPBP intramembrane metalloprotease

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CPBP intramembrane metalloprotease Provide feedback

This family includes eukaryotic type II CAAX prenyl proteases and their related bacterial and archaeal homologs. A member of this family was originally identified as the product of an open reading frame (orfX) upstream of two genes (abiGi and abiGii) involved in an abortive infection system, hence it was previously known as ABI. However, inactivation of this CPBP member (OrfX) suggests that it is not involved in the abortive infection mechanism. CPBP, PrsW proteases, YhfC intramembrane metalloprotease and APH-1 families are distantly related. They share four predicted core transmembrane segments and possess similar, yet distinct sets of sequence motifs. However, most of the CPBP family members contain several additional predicted transmembrane segments at the N-terminus and some members possess an additional predicted transmembrane segment at the C-terminus. For the majority of the CPBP family, the sequence motifs are: EExxxR, FxxxH, sxxxs, and HxxxB, from N- to C-termimus. Site-directed mutagenesis of the conserved glutamates and histidines (E156A or E157A in the first motif, H194A in the second motif, or H248A in the fourth motif) in yeast type II CAAX protease Rce1p, inactivated Rce1p’s enzymatic activity. Furthermore, for the Lactobacillus sakei immunity protein SkkI, double mutants of the two conserved glutamates (E133A/E134A or E133Q/E134Q) in the first motif or a single mutant of the conserved histidine in the fourth motif (H214D) lost their ability to confer immunity [1].

Literature references

  1. Pei J, Mitchell DA, Dixon JE, Grishin NV;, J Mol Biol. 2011;410:18-26.: Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1. PUBMED:21570408 EPMC:21570408


This tab holds annotation information from the InterPro database.

InterPro entry IPR003675

Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the SWISSPROT CAAX prenyl protease [PUBMED:9065405]. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding [PUBMED:11343912].

While these proteins are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity [PUBMED:20154137]. This family also includes lysostaphin resistance protein A [PUBMED:16923896].

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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Pfam Clan

This family is a member of clan Peptidase_U (CL0472), which has the following description:

This superfamily includes proteins classed as clan U by the MEROPS database. The proteins are membrane bound peptidases. The clan also includes Pfam:PF10086 which is a related family of uncharacterised proteins.

The clan contains the following 4 members:

Aph-1 CPBP PrsW-protease YhfC

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, 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. 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
(789)
Full
(20054)
Representative proteomes UniProt
(56810)
NCBI
(86852)
Meta
(1271)
RP15
(4991)
RP35
(13356)
RP55
(20110)
RP75
(28129)
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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
(789)
Full
(20054)
Representative proteomes UniProt
(56810)
NCBI
(86852)
Meta
(1271)
RP15
(4991)
RP35
(13356)
RP55
(20110)
RP75
(28129)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(789)
Full
(20054)
Representative proteomes UniProt
(56810)
NCBI
(86852)
Meta
(1271)
RP15
(4991)
RP35
(13356)
RP55
(20110)
RP75
(28129)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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_1073 (release 5.4)
Previous IDs: Abi;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Bashton M , El-Gebali S
Number in seed: 789
Number in full: 20054
Average length of the domain: 120.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 42.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 92
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 CPBP domain has been found. There are 4 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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