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Protein

PWWP domain-containing protein 1

Gene

pdp1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Necessary for DNA damage checkpoint activation. Required for the association of set9 with chromatin and subsequent methylation of H4K20. Associates with H4K20me1 to increase the concentration of set9 on chromatin to perform H4K20me3. H4K20me3 is mainly enriched at heterochromatin and is required for proper heterochromatin assembly.1 Publication

GO - Molecular functioni

  • double-stranded DNA binding Source: PomBase
  • H4K20me3 modified histone binding Source: PomBase
  • histone binding Source: PomBase
  • methylated histone binding Source: PomBase
  • nucleosomal DNA binding Source: PomBase
  • nucleosomal histone binding Source: PomBase

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

DNA damage

Names & Taxonomyi

Protein namesi
Recommended name:
PWWP domain-containing protein 1
Alternative name(s):
Set9-associated factor pdp1
Gene namesi
Name:pdp1
ORF Names:SPBC29A3.13
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC29A3.13.
PomBaseiSPBC29A3.13. pdp1.

Subcellular locationi

GO - Cellular componenti

  • nuclear chromatin Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi66 – 661W → A: Reduces the association of set9 with nucleosome and the H4K20me3 levels. 1 Publication
Mutagenesisi94 – 941F → A: Reduces the association of set9 with nucleosome and the H4K20me3 levels. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 359359PWWP domain-containing protein 1PRO_0000303950Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei252 – 2521Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO59676.

PTM databases

iPTMnetiO59676.

Interactioni

Subunit structurei

Interacts with set9 and histone H4K20me1. Associates with nucleosomes.1 Publication

GO - Molecular functioni

  • H4K20me3 modified histone binding Source: PomBase
  • histone binding Source: PomBase
  • methylated histone binding Source: PomBase
  • nucleosomal DNA binding Source: PomBase
  • nucleosomal histone binding Source: PomBase

Protein-protein interaction databases

BioGridi276883. 48 interactions.
MINTiMINT-4675368.

Structurei

Secondary structure

1
359
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi54 – 596Combined sources
Beta strandi61 – 633Combined sources
Beta strandi65 – 8016Combined sources
Beta strandi82 – 843Combined sources
Beta strandi86 – 949Combined sources
Turni95 – 984Combined sources
Beta strandi99 – 1035Combined sources
Helixi105 – 1073Combined sources
Beta strandi108 – 1103Combined sources
Helixi113 – 1219Combined sources
Beta strandi123 – 1253Combined sources
Helixi128 – 13710Combined sources
Helixi140 – 1423Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L89NMR-A45-152[»]
ProteinModelPortaliO59676.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini52 – 11463PWWPPROSITE-ProRule annotationAdd
BLAST

Domaini

The C-terminal region mediates association with set9, whereas the N-terminal PWWP domain recognizes H4K20me1.1 Publication

Sequence similaritiesi

Contains 1 PWWP domain.PROSITE-ProRule annotation

Phylogenomic databases

InParanoidiO59676.
OMAiTSISEMY.
OrthoDBiEOG7ZGXCW.
PhylomeDBiO59676.

Family and domain databases

InterProiIPR000313. PWWP_dom.
[Graphical view]
PfamiPF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00293. PWWP. 1 hit.
[Graphical view]
PROSITEiPS50812. PWWP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O59676-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNNARTNAKR RRLSSKQGGL SISEGKESNI PSVVEESKDN LEQASADDRL
60 70 80 90 100
NFGDRILVKA PGYPWWPALL LRRKETKDSL NTNSSFNVLY KVLFFPDFNF
110 120 130 140 150
AWVKRNSVKP LLDSEIAKFL GSSKRKSKEL IEAYEASKTP PDLKEESSTD
160 170 180 190 200
EEMDSLSAAE EKPNFLQKRK YHWETSLDES DAESISSGSL MSITSISEMY
210 220 230 240 250
GPTVASTSRS STQLSDQRYP LSSNFDHRGE AKGKGKQPLK NPQERGRISP
260 270 280 290 300
SSPLNDQTKA LMQRLLFFRH KLQKAFLSPD HLIVEEDFYN ASKYLNAISD
310 320 330 340 350
IPFLNYELIT STKLAKVLKR IAFLEHLEND ELYDIRQKCK NLLYSWAMFL

PNEPSIKGM
Length:359
Mass (Da):40,923
Last modified:August 1, 1998 - v1
Checksum:iA892EE06E5F7DB2A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA18390.1.
AB027814 Genomic DNA. Translation: BAA87118.1.
PIRiT40084.
RefSeqiNP_595841.1. NM_001021745.2.

Genome annotation databases

EnsemblFungiiSPBC29A3.13.1; SPBC29A3.13.1:pep; SPBC29A3.13.
GeneIDi2540354.
KEGGispo:SPBC29A3.13.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAA18390.1.
AB027814 Genomic DNA. Translation: BAA87118.1.
PIRiT40084.
RefSeqiNP_595841.1. NM_001021745.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2L89NMR-A45-152[»]
ProteinModelPortaliO59676.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi276883. 48 interactions.
MINTiMINT-4675368.

PTM databases

iPTMnetiO59676.

Proteomic databases

MaxQBiO59676.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC29A3.13.1; SPBC29A3.13.1:pep; SPBC29A3.13.
GeneIDi2540354.
KEGGispo:SPBC29A3.13.

Organism-specific databases

EuPathDBiFungiDB:SPBC29A3.13.
PomBaseiSPBC29A3.13. pdp1.

Phylogenomic databases

InParanoidiO59676.
OMAiTSISEMY.
OrthoDBiEOG7ZGXCW.
PhylomeDBiO59676.

Miscellaneous databases

PROiO59676.

Family and domain databases

InterProiIPR000313. PWWP_dom.
[Graphical view]
PfamiPF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00293. PWWP. 1 hit.
[Graphical view]
PROSITEiPS50812. PWWP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion genomic DNA library."
    Ding D.-Q., Tomita Y., Yamamoto A., Chikashige Y., Haraguchi T., Hiraoka Y.
    Genes Cells 5:169-190(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 9-189, SUBCELLULAR LOCATION.
    Strain: ATCC 38364 / 968.
  3. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-252, IDENTIFICATION BY MASS SPECTROMETRY.
  5. "Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein."
    Wang Y., Reddy B., Thompson J., Wang H., Noma K., Yates J.R. III, Jia S.
    Mol. Cell 33:428-437(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH SET9, HISTONE-BINDING, FUNCTION, DOMAIN, MUTAGENESIS OF TRP-66 AND PHE-94.

Entry informationi

Entry nameiPDP1_SCHPO
AccessioniPrimary (citable) accession number: O59676
Secondary accession number(s): Q9USE8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: August 1, 1998
Last modified: June 8, 2016
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.