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154  structures 1380  species 0  interactions 14707  sequences 333  architectures

Family: PWWP (PF00855)

Summary: PWWP domain

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.

PWWP domain Provide feedback

The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression [2].

Literature references

  1. Stec I, Wright TJ, van Ommen GJB, de Boer PAJ, van Haeringen A, Moorman AFM, Altherr MR, den Dunnen JT; , Hum Mol Genet 1998;7:1071-1082.: WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. PUBMED:9618163 EPMC:9618163

  2. Wang Y, Reddy B, Thompson J, Wang H, Noma K, Yates JR 3rd, Jia S;, Mol Cell. 2009;33:428-437.: Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. PUBMED:19250904 EPMC:19250904

  3. Qiu C, Sawada K, Zhang X, Cheng X;, Nat Struct Biol. 2002;9:217-224.: The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. PUBMED:11836534 EPMC:11836534


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000313

The PWWP domain is an around 70 amino acids domain that was named after its central core 'Pro-Trp-Trp-Pro'. The PWWP domain is found in one or, less frequently, in two copies in nuclear, often DNA-binding proteins that function as transcription factors regulating developmental processes. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present, it has been proposed that the PWWP domain is involved in protein-protein interactions [ PUBMED:10802047 , PUBMED:28645917 ]. The structure of the PWWP domain comprises a five-stranded beta-barrel followed by a five-helix bundle [ PUBMED:11836534 ].

Conservation of the PWWP domain is concentrated on one major and two minor blocks with length differences occurring in between [ PUBMED:10802047 ].

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 Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 33 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_2 Chromo_shadow Cul7 DUF1325 DUF4537 DUF4819 GEN1_C Hva1_TUDOR LBR_tudor LytTR MBT Mtf2_C ProQ_C PWWP Rad9_Rad53_bind RBB1NT SAWADEE SMN SNase TTD TUDOR Tudor-knot Tudor_1_RapA Tudor_2 Tudor_3 Tudor_4 Tudor_5 Tudor_FRX1 Tudor_RapA

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
(198)
Full
(14707)
Representative proteomes UniProt
(24942)
RP15
(1789)
RP35
(5641)
RP55
(12322)
RP75
(16998)
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HTML View             
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
(198)
Full
(14707)
Representative proteomes UniProt
(24942)
RP15
(1789)
RP35
(5641)
RP55
(12322)
RP75
(16998)
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
(198)
Full
(14707)
Representative proteomes UniProt
(24942)
RP15
(1789)
RP35
(5641)
RP55
(12322)
RP75
(16998)
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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 198
Number in full: 14707
Average length of the domain: 92.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 11.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.6 25.6
Noise cut-off 25.5 25.5
Model length: 93
Family (HMM) version: 19
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 PWWP domain has been found. There are 154 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
A0A096R4D2 View 3D Structure Click here
A0A096RLJ2 View 3D Structure Click here
A0A096SC75 View 3D Structure Click here
A0A0G2K001 View 3D Structure Click here
A0A0G2K001 View 3D Structure Click here
A0A0G2K432 View 3D Structure Click here
A0A0P0V603 View 3D Structure Click here
A0A0P0VXN2 View 3D Structure Click here
A0A0P0WHB3 View 3D Structure Click here
A0A0P0WI45 View 3D Structure Click here
A0A0P0WNF2 View 3D Structure Click here
A0A0P0WNI4 View 3D Structure Click here
A0A0R0EQM1 View 3D Structure Click here
A0A0R0EQU1 View 3D Structure Click here
A0A0R0GVB6 View 3D Structure Click here
A0A0R0HDU9 View 3D Structure Click here
A0A0R0IPK3 View 3D Structure Click here
A0A0R0JPK7 View 3D Structure Click here
A0A0R4IAE0 View 3D Structure Click here
A0A0R4IGL9 View 3D Structure Click here
A0A0R4IS80 View 3D Structure Click here
A0A0R4IXV5 View 3D Structure Click here
A0A1D6FGS6 View 3D Structure Click here
A0A1D6FRX1 View 3D Structure Click here
A0A1D6FUK3 View 3D Structure Click here
A0A1D6FXH9 View 3D Structure Click here
A0A1D6G0P9 View 3D Structure Click here
A0A1D6HH07 View 3D Structure Click here
A0A1D6I0U5 View 3D Structure Click here
A0A1D6IPI9 View 3D Structure Click here
A0A1D6J298 View 3D Structure Click here
A0A1D6K3N5 View 3D Structure Click here
A0A1D6KLE2 View 3D Structure Click here
A0A1D6M648 View 3D Structure Click here
A0A1D6MDX6 View 3D Structure Click here
A0A1D6MFV1 View 3D Structure Click here
A0A1D6NMK7 View 3D Structure Click here
A0A1D6P9K0 View 3D Structure Click here
A0A1D6QJJ2 View 3D Structure Click here
A0A1D8PQR7 View 3D Structure Click here
A0A1I9LTU3 View 3D Structure Click here
A0A1X7YFR6 View 3D Structure Click here
A0A2R8QFE1 View 3D Structure Click here
A0A2R8QFE1 View 3D Structure Click here
A0A2R8QIN7 View 3D Structure Click here
A0A2R8QLT8 View 3D Structure Click here
A0A2R8QTI0 View 3D Structure Click here
A0A2R8QTI0 View 3D Structure Click here
A0A368UGE2 View 3D Structure Click here
A2A484 View 3D Structure Click here
A4I9C3 View 3D Structure Click here
A8C4G9 View 3D Structure Click here
B2KF05 View 3D Structure Click here
B2RRD7 View 3D Structure Click here
B8JIA4 View 3D Structure Click here
B8JIA4 View 3D Structure Click here
B8JLQ7 View 3D Structure Click here
D3ZMD3 View 3D Structure Click here
D3ZUW8 View 3D Structure Click here
D4A0U9 View 3D Structure Click here
D4A411 View 3D Structure Click here
D4A9J4 View 3D Structure Click here
D4A9J4 View 3D Structure Click here
D4AA06 View 3D Structure Click here
D4AA06 View 3D Structure Click here
E7F6H4 View 3D Structure Click here
E7FDX0 View 3D Structure Click here
E9Q9M8 View 3D Structure Click here
F1LT90 View 3D Structure Click here
F1M2K1 View 3D Structure Click here
F1Q9U9 View 3D Structure Click here
F1Q9U9 View 3D Structure Click here
F1QFR1 View 3D Structure Click here
F1QYK7 View 3D Structure Click here
F1R1K5 View 3D Structure Click here
F1R4W7 View 3D Structure Click here
F4IN78 View 3D Structure Click here
F4IXJ0 View 3D Structure Click here
F4IZM8 View 3D Structure Click here
F4K4D6 View 3D Structure Click here
F6P390 View 3D Structure Click here
F7FKH2 View 3D Structure Click here
G5E8P1 View 3D Structure Click here
H9GXF8 View 3D Structure Click here
I1JAI6 View 3D Structure Click here
I1JFC3 View 3D Structure Click here
I1JNS1 View 3D Structure Click here
I1JPS7 View 3D Structure Click here
I1JV29 View 3D Structure Click here
I1JYS9 View 3D Structure Click here
I1KAR4 View 3D Structure Click here
I1KGF6 View 3D Structure Click here
I1KHV6 View 3D Structure Click here
I1KWS1 View 3D Structure Click here
I1LBA8 View 3D Structure Click here
I1LIJ1 View 3D Structure Click here
I1NAD7 View 3D Structure Click here
K7K770 View 3D Structure Click here
K7KGC4 View 3D Structure Click here
K7KU48 View 3D Structure Click here
K7LH02 View 3D Structure Click here
K7LHH9 View 3D Structure Click here
K7LIT1 View 3D Structure Click here
K7LMH0 View 3D Structure Click here
K7LNW8 View 3D Structure Click here
K7LSJ6 View 3D Structure Click here
K7MEU6 View 3D Structure Click here
K7MFP9 View 3D Structure Click here
K7MRP8 View 3D Structure Click here
K7MV89 View 3D Structure Click here
K7MVS3 View 3D Structure Click here
K7MWZ2 View 3D Structure Click here
K7MYJ3 View 3D Structure Click here
K7MZX8 View 3D Structure Click here
K7N598 View 3D Structure Click here
K7UY21 View 3D Structure Click here
K7V562 View 3D Structure Click here
K7VXY0 View 3D Structure Click here
M0RC55 View 3D Structure Click here
O59676 View 3D Structure Click here
O75475 View 3D Structure Click here
O88491 View 3D Structure Click here
O88508 View 3D Structure Click here
O88509 View 3D Structure Click here
O94312 View 3D Structure Click here
O95696 View 3D Structure Click here
O96028 View 3D Structure Click here
O96028 View 3D Structure Click here
P0CB22 View 3D Structure Click here
P51858 View 3D Structure Click here
P51859 View 3D Structure Click here
P52701 View 3D Structure Click here
P54276 View 3D Structure Click here
P55201 View 3D Structure Click here
P59278 View 3D Structure Click here
Q04213 View 3D Structure Click here
Q06188 View 3D Structure Click here
Q08EN7 View 3D Structure Click here
Q09842 View 3D Structure Click here
Q0D412 View 3D Structure Click here
Q15326 View 3D Structure Click here
Q1LZ51 View 3D Structure Click here
Q1LZ53 View 3D Structure Click here
Q2VPR5 View 3D Structure Click here
Q3UMU9 View 3D Structure Click here
Q49A26 View 3D Structure Click here
Q4CXN6 View 3D Structure Click here
Q4CXN7 View 3D Structure Click here
Q4DEC4 View 3D Structure Click here
Q4DEC5 View 3D Structure Click here
Q504Y3 View 3D Structure Click here
Q54GE4 View 3D Structure Click here
Q54HN1 View 3D Structure Click here
Q54VR9 View 3D Structure Click here
Q588C6 View 3D Structure Click here
Q5A4L3 View 3D Structure Click here
Q5NAU3 View 3D Structure Click here
Q5NAU4 View 3D Structure Click here
Q5RKH0 View 3D Structure Click here
Q5RKN4 View 3D Structure Click here
Q5TGJ6 View 3D Structure Click here
Q5TYK5 View 3D Structure Click here
Q5XXA7 View 3D Structure Click here
Q69Z61 View 3D Structure Click here
Q6IR42 View 3D Structure Click here
Q6K431 View 3D Structure Click here
Q6NUJ5 View 3D Structure Click here
Q6P2L6 View 3D Structure Click here
Q6P2L6 View 3D Structure Click here
Q6Z1Z8 View 3D Structure Click here
Q6Z3Y5 View 3D Structure Click here
Q6Z8D4 View 3D Structure Click here
Q6ZJC9 View 3D Structure Click here
Q75JG1 View 3D Structure Click here
Q7JVP4 View 3D Structure Click here
Q7K264 View 3D Structure Click here
Q7Z4V5 View 3D Structure Click here
Q812D1 View 3D Structure Click here
Q8BVE8 View 3D Structure Click here
Q8BVE8 View 3D Structure Click here
Q8GZ42 View 3D Structure Click here
Q8MT36 View 3D Structure Click here
Q8MT36 View 3D Structure Click here
Q8R5C8 View 3D Structure Click here
Q8S9U1 View 3D Structure Click here
Q8T079 View 3D Structure Click here
Q8VHK7 View 3D Structure Click here
Q922P9 View 3D Structure Click here
Q923W4 View 3D Structure Click here
Q925G1 View 3D Structure Click here
Q96L73 View 3D Structure Click here
Q96L73 View 3D Structure Click here
Q96N64 View 3D Structure Click here
Q99JF8 View 3D Structure Click here
Q9BZ95 View 3D Structure Click here
Q9BZ95 View 3D Structure Click here
Q9C5X4 View 3D Structure Click here
Q9FNE4 View 3D Structure Click here
Q9H0M4 View 3D Structure Click here
Q9JMG7 View 3D Structure Click here
Q9LEY4 View 3D Structure Click here
Q9LK91 View 3D Structure Click here
Q9LYZ0 View 3D Structure Click here
Q9M364 View 3D Structure Click here
Q9M9N3 View 3D Structure Click here
Q9MA56 View 3D Structure Click here
Q9SF36 View 3D Structure Click here
Q9SUE7 View 3D Structure Click here
Q9UBC3 View 3D Structure Click here
Q9ULD4 View 3D Structure Click here
Q9ULU4 View 3D Structure Click here
Q9VAA9 View 3D Structure Click here
Q9VFP7 View 3D Structure Click here
Q9VWH5 View 3D Structure Click here
Q9XER9 View 3D Structure Click here
Q9Y3E1 View 3D Structure Click here
Q9Y6K1 View 3D Structure Click here