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64  structures 201  species 2  interactions 329  sequences 6  architectures

Family: POT1 (PF02765)

Summary: Telomeric single stranded DNA binding POT1/CDC13

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Telomeric single stranded DNA binding POT1/CDC13 Provide feedback

This domain binds single stranded telomeric DNA and adopts an OB fold [1]. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [2-4]. POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms [5,6].

Literature references

  1. Mitton-Fry RM, Anderson EM, Hughes TR, Lundblad V, Wuttke DS; , Science. 2002;296:145-147.: Conserved structure for single-stranded telomeric DNA recognition. PUBMED:11935027 EPMC:11935027

  2. Chandra A, Hughes TR, Nugent CI, Lundblad V; , Genes Dev. 2001;15:404-414.: Cdc13 both positively and negatively regulates telomere replication. PUBMED:11230149 EPMC:11230149

  3. Churikov D, Price CM; , Nat Struct Mol Biol. 2008;15:79-84.: Pot1 and cell cycle progression cooperate in telomere length regulation. PUBMED:18066078 EPMC:18066078

  4. Churikov D, Wei C, Price CM; , Mol Cell Biol. 2006;26:6971-6982.: Vertebrate POT1 restricts G-overhang length and prevents activation of a telomeric DNA damage checkpoint but is dispensable for overhang protection. PUBMED:16943437 EPMC:16943437

  5. Le-Van-Dien, Kikot' BS, Savinskaia AP;, Vopr Onkol. 1975;21:16-18.: [Use of infrared and ultraviolet absorption spectra in the analysis of mixtures in polysaccharide complexes from the tissues of metastases from chorioepithelioma of the uterus]. PUBMED:1239117 EPMC:1239117

  6. Shakirov EV, McKnight TD, Shippen DE;, Plant J. 2009;58:1004-1015.: POT1-independent single-strand telomeric DNA binding activities in Brassicaceae. PUBMED:19228335 EPMC:19228335

  7. de Lange T;, Genes Dev. 2005;19:2100-2110.: Shelterin: the protein complex that shapes and safeguards human telomeres. PUBMED:16166375 EPMC:16166375


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011564

This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold [PUBMED:11935027]. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [PUBMED:11230149, PUBMED:18066078, PUBMED:16943437].

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
(48)
Full
(329)
Representative proteomes NCBI
(352)
Meta
(3)
RP15
(42)
RP35
(85)
RP55
(131)
RP75
(177)
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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
(48)
Full
(329)
Representative proteomes NCBI
(352)
Meta
(3)
RP15
(42)
RP35
(85)
RP55
(131)
RP75
(177)
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
(48)
Full
(329)
Representative proteomes NCBI
(352)
Meta
(3)
RP15
(42)
RP35
(85)
RP55
(131)
RP75
(177)
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.

Pfam alignments:

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: pdb_1s40
Previous IDs: Telo_bind;
Type: Domain
Author: Mian N, Bateman A, Griffiths-Jones SR, Sammut SJ, Wood V, Mistry J
Number in seed: 48
Number in full: 329
Average length of the domain: 138.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 19.57 %

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 21.1 21.1
Trusted cut-off 21.4 21.4
Noise cut-off 21.0 21.0
Model length: 146
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

POT1 TEBP_beta

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 POT1 domain has been found. There are 64 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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