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20  structures 2033  species 0  interactions 2772  sequences 74  architectures

Family: PNK3P (PF08645)

Summary: Polynucleotide kinase 3 phosphatase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

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 [1].

Literature references

  1. 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

  2. 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

  3. 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

  4. 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

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 25 members:

5_nucleotid Acid_phosphat_B Acid_PPase APP1_cat Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PhoLip_ATPase_C PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

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 and the UniProtKB 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
(2772)
Representative proteomes UniProt
(7596)
RP15
(561)
RP35
(1261)
RP55
(2279)
RP75
(3468)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(24)
Full
(2772)
Representative proteomes UniProt
(7596)
RP15
(561)
RP35
(1261)
RP55
(2279)
RP75
(3468)
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
(24)
Full
(2772)
Representative proteomes UniProt
(7596)
RP15
(561)
RP35
(1261)
RP55
(2279)
RP75
(3468)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_6220 (release 19.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Wood V
Number in seed: 24
Number in full: 2772
Average length of the domain: 153.3 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 38.08 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 162
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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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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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044TQJ3 View 3D Structure Click here
A0A077ZGA0 View 3D Structure Click here
A0A0D2HNC7 View 3D Structure Click here
A0A0G2JUH4 View 3D Structure Click here
A0A0H3GV71 View 3D Structure Click here
A0A0K0EE81 View 3D Structure Click here
A0A0N4UJA1 View 3D Structure Click here
A0A0P0V7Y1 View 3D Structure Click here
A0A0P0V7Y6 View 3D Structure Click here
A0A175VXS6 View 3D Structure Click here
A0A1C1CTQ1 View 3D Structure Click here
A0A1D6ML44 View 3D Structure Click here
A0A1D6ND74 View 3D Structure Click here
A0A1D8PGJ5 View 3D Structure Click here
A0A2R8QSN3 View 3D Structure Click here
A0A3P7E3C3 View 3D Structure Click here
A0A5K4F620 View 3D Structure Click here
A6TBC5 View 3D Structure Click here
A8PZ02 View 3D Structure Click here
B2FPM1 View 3D Structure Click here
C0H4V3 View 3D Structure Click here
C0NGB8 View 3D Structure Click here
C1HAJ7 View 3D Structure Click here
I1KDK7 View 3D Structure Click here
K7LUT0 View 3D Structure Click here
O13911 View 3D Structure Click here
P57203 View 3D Structure Click here
P59454 View 3D Structure Click here
P62455 View 3D Structure Click here
Q03796 View 3D Structure Click here
Q19683 View 3D Structure Click here
Q32EF1 View 3D Structure Click here
Q47XB6 View 3D Structure Click here
Q4CZY2 View 3D Structure Click here
Q4DFE1 View 3D Structure Click here
Q4DQH2 View 3D Structure Click here
Q4E1V6 View 3D Structure Click here
Q54U78 View 3D Structure Click here
Q585Q2 View 3D Structure Click here
Q6TG07 View 3D Structure Click here