Summary: Polynucleotide kinase 3 phosphatase
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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.
Polynucleotide kinase 3 phosphatase Provide feedback
Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin [3].
Literature references
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Meijer M, Karimi-Busheri F, Huang TY, Weinfeld M, Young D; , J Biol Chem. 2002;277:4050-4055.: Pnk1, a DNA kinase/phosphatase required for normal response to DNA damage by gamma-radiation or camptothecin in Schizosaccharomyces pombe. PUBMED:11729194 EPMC:11729194
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Jilani A, Ramotar D; , Biochemistry. 2002;41:7688-7694.: Purification and partial characterization of a DNA 3'-phosphatase from Schizosaccharomyces pombe. PUBMED:12056900 EPMC:12056900
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Meijer M, Karimi-Busheri F, Huang TY, Weinfeld M, Young D; , J Biol Chem. 2002;277:4050-4055.: Pnk1, a DNA kinase/phosphatase required for normal response to DNA damage by gamma-radiation or camptothecin in Schizosaccharomyces pombe. PUBMED:11729194 EPMC:11729194
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Vance JR, Wilson TE; , J Biol Chem. 2001;276:15073-15081.: Uncoupling of 3'-phosphatase and 5'-kinase functions in budding yeast. Characterization of Saccharomyces cerevisiae DNA 3'-phosphatase (TPP1). PUBMED:11278831 EPMC:11278831
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Karimi-Busheri F, Daly G, Robins P, Canas B, Pappin DJ, Sgouros J, Miller GG, Fakhrai H, Davis EM, Le Beau MM, Weinfeld M; , J Biol Chem. 1999;274:24187-24194.: Molecular characterization of a human DNA kinase. PUBMED:10446193 EPMC:10446193
Internal database links
SCOOP: | HAD HAD_2 Hydrolase Hydrolase_6 Hydrolase_like |
Similarity to PfamA using HHSearch: | Hydrolase Hydrolase_3 PGP_phosphatase HAD Hydrolase_like Hydrolase_6 HAD_2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013954
Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin [PUBMED:11729194].
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 HAD (CL0137), which has the following description:
This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].
The clan contains the following 23 members:
5_nucleotid Acid_phosphat_B Acid_PPase Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1Alignments
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 (24) |
Full (2135) |
Representative proteomes | UniProt (6575) |
NCBI (26164) |
Meta (716) |
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RP15 (392) |
RP35 (954) |
RP55 (1692) |
RP75 (2726) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (24) |
Full (2135) |
Representative proteomes | UniProt (6575) |
NCBI (26164) |
Meta (716) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (392) |
RP35 (954) |
RP55 (1692) |
RP75 (2726) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_6220 (release 19.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Mistry J |
Number in seed: | 24 |
Number in full: | 2135 |
Average length of the domain: | 154.20 aa |
Average identity of full alignment: | 29 % |
Average coverage of the sequence by the domain: | 39.41 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 162 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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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 PNK3P domain has been found. There are 20 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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