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932  structures 2879  species 26  interactions 55769  sequences 1408  architectures

Family: PDZ (PF00595)

Summary: PDZ domain

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 "PDZ domain". More...

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.

PDZ domain Provide feedback

PDZ domains are found in diverse signaling proteins.

Literature references

  1. Ponting CP, Phillips C, Davies KE, Blake DJ , Bioessays 1997;19:469-479.: PDZ domains: targeting signalling molecules to sub-membranous sites. PUBMED:9204764 EPMC:9204764

  2. Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R; , Cell. 1996;85:1067-1076.: Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. PUBMED:8674113 EPMC:8674113

  3. Ponting CP; , Protein Sci 1997;6:464-468.: Evidence for PDZ domains in bacteria, yeast, and plants. PUBMED:9041651 EPMC:9041651

  4. Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS;, Sci Signal. 2009;2:ra50.: Rapid evolution of functional complexity in a domain family. PUBMED:19738200 EPMC:19738200


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001478

PDZ domains (also known as Discs-large homologous regions (DHR) or GLGF)) are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [PUBMED:9041651, PUBMED:9204764]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences [PUBMED:9204764]. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated.

PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.

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 PDZ-like (CL0466), which has the following description:

This superfamily comprises families of PDZ domains, which are peptide binding sites.

The clan contains the following 10 members:

EBP50_C GRASP55_65 PDZ PDZ_1 PDZ_2 PDZ_3 PDZ_4 PDZ_5 PDZ_6 Tricorn_PDZ

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...

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
(44)
Full
(55769)
Representative proteomes UniProt
(96792)
NCBI
(380661)
Meta
(6191)
RP15
(9952)
RP35
(20470)
RP55
(35741)
RP75
(44322)
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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
(44)
Full
(55769)
Representative proteomes UniProt
(96792)
NCBI
(380661)
Meta
(6191)
RP15
(9952)
RP35
(20470)
RP55
(35741)
RP75
(44322)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(44)
Full
(55769)
Representative proteomes UniProt
(96792)
NCBI
(380661)
Meta
(6191)
RP15
(9952)
RP35
(20470)
RP55
(35741)
RP75
(44322)
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.

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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 44
Number in full: 55769
Average length of the domain: 80.90 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 15.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.2 23.2
Trusted cut-off 23.2 23.2
Noise cut-off 23.1 23.1
Model length: 82
Family (HMM) version: 24
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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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 are 26 interactions for this family. More...

Porin_1 Syndecan Trypsin NMDAR2_C EBP50_C Cadherin_C DUF4136 SH3_2 PDZ SAM_1 Ras Trypsin_2 Lys PDZ_assoc Trypsin_2 MAGUK_N_PEST EB1_binding Porin_1 Trypsin Peptidase_M50 SH3_2 Peptidase_M50 PDZ_assoc MAGUK_N_PEST Metallophos PID

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 PDZ domain has been found. There are 932 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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