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2  structures 122  species 1  interaction 3533  sequences 54  architectures

Family: PPE (PF00823)

Summary: PPE family

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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.

PPE family Provide feedback

This family named after a PPE motif near to the amino terminus of the domain. The PPE family of proteins all contain an amino-terminal region of about 180 amino acids. The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups. The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are only related in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [1].

Literature references

  1. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jage, Nature 1998;393:537-544.: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. PUBMED:9634230 EPMC:9634230

  2. Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D; , Proc Natl Acad Sci U S A. 2006;103:8060-8065.: Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. PUBMED:16690741 EPMC:16690741


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000030

The human pathogen Mycobacterium tuberculosis harbours a large number of genes that encode proteins whose N-termini contain the characteristic motifs Pro-Glu (PE) or Pro-Pro-Glu (PPE). A subgroup of the PE proteins contains polymorphic GC-rich sequences (PGRS), while a subgroup of the PPE proteins contains major polymorphic tandem repeats (MPTR). The function of most of these proteins remains unknown [PUBMED:19602151]. However, the PE_PGRS proteins from Mycobacterium marinum are secreted by components of the ESX-5 system that belongs to the recently defined type VII secretion systems [PUBMED:18981138]. It has also been reported that the PE_PGRS family of proteins contains multiple calcium-binding and glycine-rich sequence motifs GGXGXD/NXUX. This sequence repeat constitutes a calcium-binding parallel beta-roll or parallel beta-helix structure and is found in RTX toxins secreted by many Gram-negative bacteria [PUBMED:18267304].

This mycobacterial family is named after a conserved amino-terminal region of about 180 amino acids, the PPE motif. The carboxy termini of proteins belonging to the PPE family are variable, and on the basis of this region at least three groups can be distinguished. The MPTR subgroup is characterised by tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group shares only similarity in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [PUBMED:9634230].

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 EsxAB (CL0352), which has the following description:

The WXG100 protein secretion system (Wss) is responsible for the secretion of WXG100 proteins (PF06013), such as ESAT-10 (6 kDa early secreted antigenic target) and CFP-10 (10 kDa culture filtrate protein) in Mycobacterium tuberculosis or EsxA (ESAT-6-like extracellularly secreted protein A) and EsxB in Staphylococcus aureus. These two proteins, generally encoded in the same gene cluster, form a 1:1 heterodimeric complex. These proteins are virulence factors involved in host-pathogen interaction [1], as demonstrated in Mycobacterium tuberculosis, Staphylococcus aureus or Bacillus anthracis. The Wss is encoded in many other Gram-positive (monoderm) bacteria. This superfamily contains a number of DUFs which are closely related and may or may not represent the same family of proteins.

The clan contains the following 6 members:

DUF2563 DUF2580 LXG PE PPE WXG100

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(146)
Full
(3533)
Representative proteomes NCBI
(2191)
Meta
(1)
RP15
(97)
RP35
(190)
RP55
(347)
RP75
(395)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(146)
Full
(3533)
Representative proteomes NCBI
(2191)
Meta
(1)
RP15
(97)
RP35
(190)
RP55
(347)
RP75
(395)
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
(146)
Full
(3533)
Representative proteomes NCBI
(2191)
Meta
(1)
RP15
(97)
RP35
(190)
RP55
(347)
RP75
(395)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_297 (release 3.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 146
Number in full: 3533
Average length of the domain: 151.60 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 28.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 159
Family (HMM) version: 14
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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Interactions

There is 1 interaction for this family. More...

PE

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 PPE domain has been found. There are 2 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 seqence.

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