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Protein

RNA polymerase II degradation factor 1

Gene

DEF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

GO - Biological processi

  • cellular response to DNA damage stimulus Source: SGD
  • protein ubiquitination Source: SGD
  • telomere maintenance Source: SGD
  • transcription-coupled nucleotide-excision repair Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL054C.
SGDiS000001537. DEF1.

Subcellular locationi

GO - Cellular componenti

  • chromosome, telomeric region Source: UniProtKB-SubCell
  • 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 1PRO_0000203177Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei260 – 2601PhosphoserineCombined sources
Modified residuei273 – 2731PhosphoserineCombined sources
Modified residuei307 – 3071PhosphoserineCombined sources
Modified residuei338 – 3381PhosphothreonineCombined sources
Modified residuei646 – 6461PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP35732.

PTM databases

iPTMnetiP35732.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi34079. 77 interactions.
DIPiDIP-6354N.
IntActiP35732. 41 interactions.
MINTiMINT-693440.

Structurei

3D structure databases

ProteinModelPortaliP35732.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 6343CUEPROSITE-ProRule annotationAdd
BLAST

Compositional bias

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

Sequence similaritiesi

Belongs to the DEF1 family.Curated
Contains 1 CUE domain.PROSITE-ProRule annotation

Phylogenomic databases

InParanoidiP35732.
OMAiYPGMFDS.
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

        10         20         30         40         50
MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD
60 70 80 90 100
LETIIDKITS GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI
110 120 130 140 150
TYKSSNNSNS FTSTKHNSSN NYTQARNKKK VQTPRAHTTG KHVNLDKGKH
160 170 180 190 200
VPSKPVSNTT SWAAAVSVDT KHDVPQDSND NNNEELEAQG QQAQEKNQEK
210 220 230 240 250
EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK KMSWAAIATP
260 270 280 290 300
KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE
310 320 330 340 350
EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA
360 370 380 390 400
APEEEVTVVE EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ
410 420 430 440 450
QPQQPQQQQQ PQQPQQPQQQ LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ
460 470 480 490 500
QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ HPQPQSQQPQ SQQSPQSQKQ
510 520 530 540 550
GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA QNNAQTSGNA
560 570 580 590 600
NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM
610 620 630 640 650
PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG
660 670 680 690 700
VAQHSEDSQQ KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ
710 720 730
FQQQQQQAAA AAAAAAQQGV PYGYNGYDYN SKNSRGFY
Length:738
Mass (Da):83,973
Last modified:June 1, 1994 - v1
Checksum:i05734E2D0B7389AC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP35732.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34079. 77 interactions.
DIPiDIP-6354N.
IntActiP35732. 41 interactions.
MINTiMINT-693440.

PTM databases

iPTMnetiP35732.

Proteomic databases

MaxQBiP35732.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YKL054C.
SGDiS000001537. DEF1.

Phylogenomic databases

InParanoidiP35732.
OMAiYPGMFDS.
OrthoDBiEOG7Z0K6R.

Enzyme and pathway databases

BioCyciYEAST:G3O-31854-MONOMER.

Miscellaneous databases

PROiP35732.

Family and domain databases

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

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: July 6, 2016
This is version 125 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.1 Publication

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

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.