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236  structures 3183  species 8  interactions 18473  sequences 4566  architectures

Family: TPR_1 (PF00515)

Summary: Tetratricopeptide repeat

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 "Tetratricopeptide". More...

Tetratricopeptide Edit Wikipedia article

Tetratricopeptide repeat
PDB 1a17 EBI.jpg
Identifiers
Symbol TPR_1
Pfam PF00515
Pfam clan CL0020
InterPro IPR001440
SCOP 1a17
SUPERFAMILY 1a17
CDD cd00189

The tetratricopeptide repeat (TPR) is a structural motif. It consists in a degenerate 34 amino acid sequence motif identified in a wide variety of proteins. It is found in tandem arrays of 3–16 motifs,[1] which form scaffolds to mediate protein–protein interactions and often the assembly of multiprotein complexes. These repeats usually fold together to produce a single, linear solenoid domain called TPR domain. Proteins with such domains include the anaphase-promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67-phox, hsp90-binding immunophilins, transcription factors, the PKR protein kinase inhibitor, the major receptor for peroxisomal matrix protein import PEX5 and mitochondrial import proteins.

Structure[edit]

The structure of the PP5 protein was the first structure to be determined. The structure solved by X-ray crystallography by Das and colleagues showed that the TPR sequence motif was composed of a pair of antiparallel alpha helices.[2] The PP5 structure contained 3 tandem TPR repeats which showed the sequential TPR repeats formed an alpha-helical solenoid structure.

Examples[edit]

Human genes encoding proteins containing this motif include:

References[edit]

  1. ^ Blatch GL, Lässle M (November 1999). "The tetratricopeptide repeat: a structural motif mediating protein-protein interactions". BioEssays 21 (11): 932–9. doi:10.1002/(SICI)1521-1878(199911)21:11<932::AID-BIES5>3.0.CO;2-N. PMID 10517866. 
  2. ^ Das AK, Cohen PW, Barford D (March 1998). "The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions". EMBO J. 17 (5): 1192–9. doi:10.1093/emboj/17.5.1192. PMC 1170467. PMID 9482716. 

External links[edit]

Further reading[edit]

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.

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Literature references

  1. Lamb JR, Tugendreich S, Hieter P; , Trends Biochem Sci 1995;20:257-259.: Tetratrico peptide repeat interactions: to TPR or not to TPR? PUBMED:7667876 EPMC:7667876

  2. Das AK, Cohen PW, Barford D; , EMBO J 1998;17:1192-1199.: The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. PUBMED:9482716 EPMC:9482716


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001440

The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [PUBMED:7667876, PUBMED:9482716, PUBMED:1882418]. It mediates protein-protein interactions and the assembly of multiprotein complexes [PUBMED:14659697]. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices [PUBMED:14659697]. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B.

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 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
(555)
Full
(18473)
Representative proteomes NCBI
(112617)
Meta
(30616)
RP15
(3602)
RP35
(5574)
RP55
(7522)
RP75
(9338)
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PP/heatmap 1   View           
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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
(555)
Full
(18473)
Representative proteomes NCBI
(112617)
Meta
(30616)
RP15
(3602)
RP35
(5574)
RP55
(7522)
RP75
(9338)
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
(555)
Full
(18473)
Representative proteomes NCBI
(112617)
Meta
(30616)
RP15
(3602)
RP35
(5574)
RP55
(7522)
RP75
(9338)
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: Alignment kindly provided by SMART
Previous IDs: TPR;
Type: Repeat
Author: SMART
Number in seed: 555
Number in full: 18473
Average length of the domain: 31.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 6.62 %

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 22.9 13.0
Trusted cut-off 22.9 13.0
Noise cut-off 22.8 12.9
Model length: 34
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 8 interactions for this family. More...

Ras PPP5 Metallophos U-box TPR_1 FKBP_C TPR_2 SCP2

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 TPR_1 domain has been found. There are 236 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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