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P35732

- DEF1_YEAST

UniProt

P35732 - DEF1_YEAST

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Protein
RNA polymerase II degradation factor 1
Gene
DEF1, RIP1, VID31, YKL054C, YKL308
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

RNA polymerase II degradation factor recruits the ubiquitination machinery to the RNA polymerase II for polyubiquitination, removal and degradation, when RAD26 fails to efficiently displace stalled RNA polymerase II. Also involved in telomere length regulation.4 Publications

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
Complete GO annotation...

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: SGD
  2. protein ubiquitination Source: SGD
  3. telomere maintenance Source: SGD
  4. transcription-coupled nucleotide-excision repair Source: SGD
  5. ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Ubl conjugation pathway

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31854-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II degradation factor 1
Alternative name(s):
RRM3-interacting protein 1
Gene namesi
Name:DEF1
Synonyms:RIP1, VID31
Ordered Locus Names:YKL054C
ORF Names:YKL308
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XI

Organism-specific databases

CYGDiYKL054c.
SGDiS000001537. DEF1.

Subcellular locationi

Nucleus. Chromosometelomere 1 Publication

GO - Cellular componenti

  1. chromosome, telomeric region Source: UniProtKB-SubCell
  2. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus, Telomere

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 738738RNA polymerase II degradation factor 1
PRO_0000203177Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei260 – 2601Phosphoserine4 Publications
Modified residuei273 – 2731Phosphoserine1 Publication
Modified residuei307 – 3071Phosphoserine1 Publication
Modified residuei338 – 3381Phosphothreonine1 Publication
Modified residuei646 – 6461Phosphoserine3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP35732.
PaxDbiP35732.
PeptideAtlasiP35732.

Expressioni

Gene expression databases

GenevestigatoriP35732.

Interactioni

Subunit structurei

Interacts with the RNA polymerase II in a DNA-damaged dependent manner. Interacts with RAD26. Binds DNA.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself1EBI-26695,EBI-26695
ADE17P380091EBI-26695,EBI-14223
CAF40P538291EBI-26695,EBI-28306
CDC39P256551EBI-26695,EBI-12139
CPR6P536911EBI-26695,EBI-5429
CYS4P325821EBI-26695,EBI-4167
DCP2P535501EBI-26695,EBI-270
DHH1P395171EBI-26695,EBI-158
EAP1P360411EBI-26695,EBI-26995
HCH1P538341EBI-26695,EBI-28288
IPP1P008171EBI-26695,EBI-9338
LSM3P577431EBI-26695,EBI-10227
LSM4P400701EBI-26695,EBI-188
MOT2P349091EBI-26695,EBI-12174
MPT5P390161EBI-26695,EBI-2052996
PAN2P530101EBI-26695,EBI-12887
PAT1P256441EBI-26695,EBI-204
PBP1P532971EBI-26695,EBI-12961
PEX7P391081EBI-26695,EBI-13183
POP2P390081EBI-26695,EBI-13629
PUB1P325881EBI-26695,EBI-14231
PUF4P253391EBI-26695,EBI-23703
RIM1P324451EBI-26695,EBI-15206
RNR2P099381EBI-26695,EBI-15240
SLF1Q120341EBI-26695,EBI-17335
SRO9P255671EBI-26695,EBI-18084
STI1P157051EBI-26695,EBI-18418
TIP20P338911EBI-26695,EBI-19396
WHI3P347611EBI-26695,EBI-20537

Protein-protein interaction databases

BioGridi34079. 75 interactions.
DIPiDIP-6354N.
IntActiP35732. 41 interactions.
MINTiMINT-693440.
STRINGi4932.YKL054C.

Structurei

3D structure databases

ProteinModelPortaliP35732.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 6343CUE
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi382 – 718337Gln-rich
Add
BLAST
Compositional biasi574 – 5807Poly-Ala
Compositional biasi708 – 7169Poly-Ala

Sequence similaritiesi

Belongs to the DEF1 family.
Contains 1 CUE domain.

Phylogenomic databases

eggNOGiNOG16498.
OMAiWDEVKKP.
OrthoDBiEOG7Z0K6R.

Family and domain databases

InterProiIPR003892. CUE.
[Graphical view]
PfamiPF02845. CUE. 1 hit.
[Graphical view]
PROSITEiPS51140. CUE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P35732-1 [UniParc]FASTAAdd to Basket

« Hide

MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD    50
LETIIDKITS GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI 100
TYKSSNNSNS FTSTKHNSSN NYTQARNKKK VQTPRAHTTG KHVNLDKGKH 150
VPSKPVSNTT SWAAAVSVDT KHDVPQDSND NNNEELEAQG QQAQEKNQEK 200
EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK KMSWAAIATP 250
KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE 300
EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA 350
APEEEVTVVE EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ 400
QPQQPQQQQQ PQQPQQPQQQ LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ 450
QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ HPQPQSQQPQ SQQSPQSQKQ 500
GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA QNNAQTSGNA 550
NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM 600
PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG 650
VAQHSEDSQQ KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ 700
FQQQQQQAAA AAAAAAQQGV PYGYNGYDYN SKNSRGFY 738
Length:738
Mass (Da):83,973
Last modified:June 1, 1994 - v1
Checksum:i05734E2D0B7389AC
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X75781 Genomic DNA. Translation: CAA53418.1.
Z28054 Genomic DNA. Translation: CAA81890.1.
BK006944 Genomic DNA. Translation: DAA09103.1.
PIRiS37876.
RefSeqiNP_012869.1. NM_001179620.1.

Genome annotation databases

EnsemblFungiiYKL054C; YKL054C; YKL054C.
GeneIDi853811.
KEGGisce:YKL054C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X75781 Genomic DNA. Translation: CAA53418.1 .
Z28054 Genomic DNA. Translation: CAA81890.1 .
BK006944 Genomic DNA. Translation: DAA09103.1 .
PIRi S37876.
RefSeqi NP_012869.1. NM_001179620.1.

3D structure databases

ProteinModelPortali P35732.
ModBasei Search...

Protein-protein interaction databases

BioGridi 34079. 75 interactions.
DIPi DIP-6354N.
IntActi P35732. 41 interactions.
MINTi MINT-693440.
STRINGi 4932.YKL054C.

Proteomic databases

MaxQBi P35732.
PaxDbi P35732.
PeptideAtlasi P35732.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YKL054C ; YKL054C ; YKL054C .
GeneIDi 853811.
KEGGi sce:YKL054C.

Organism-specific databases

CYGDi YKL054c.
SGDi S000001537. DEF1.

Phylogenomic databases

eggNOGi NOG16498.
OMAi WDEVKKP.
OrthoDBi EOG7Z0K6R.

Enzyme and pathway databases

BioCyci YEAST:G3O-31854-MONOMER.

Miscellaneous databases

NextBioi 974978.

Gene expression databases

Genevestigatori P35732.

Family and domain databases

InterProi IPR003892. CUE.
[Graphical view ]
Pfami PF02845. CUE. 1 hit.
[Graphical view ]
PROSITEi PS51140. CUE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins."
    Rasmussen S.W.
    Yeast 10:S63-S68(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage."
    Woudstra E.C., Gilbert C., Fellows J., Jansen L., Brouwer J., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
    Nature 415:929-933(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAD26, FUNCTION.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro."
    Reid J., Svejstrup J.Q.
    J. Biol. Chem. 279:29875-29878(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RNA POLYMERASE II, FUNCTION.
  7. "Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest."
    Somesh B.P., Reid J., Liu W.F., Sogaard T.M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
    Cell 121:913-923(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Def1p is involved in telomere maintenance in budding yeast."
    Chen Y.B., Yang C.P., Li R.X., Zeng R., Zhou J.Q.
    J. Biol. Chem. 280:24784-24791(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RRM3, SUBCELLULAR LOCATION, DNA-BINDING, FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY.
  9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  10. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-273, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; THR-338 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; SER-307 AND SER-646, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiDEF1_YEAST
AccessioniPrimary (citable) accession number: P35732
Secondary accession number(s): D6VXN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: June 11, 2014
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3380 molecules/cell in log phase SD medium.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3

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