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Q03465 (RPN4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protein RPN4
Alternative name(s):
Nuclear protein SON1
Ubiquitin fusion degradation protein 5
Gene names
Name:RPN4
Synonyms:SON1, UFD5
Ordered Locus Names:YDL020C
ORF Names:D2840
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length531 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Acts as a transcriptional activator of a number of genes encoding proteasomal subunits. Binds to a PACE (proteasome-associated control element) DNA sequence 5'-GGTGGCAAA-3'. Its expression is in turn regulated by the 26S proteasome, thereby providing a negative feedback control mechanism. Required for normal growth at low temperatures. Ref.7 Ref.8

Subunit structure

Probably interacts with SEC63. Interacts with MUB1, UBR2 and RPN2. Ref.9 Ref.10

Subcellular location

Nucleus.

Post-translational modification

Ubiquitinated by UBR2 in the presence of UBC2; which leads to proteasomal degradation. Ref.9 Ref.10

Disruption phenotype

Mutants grow slowly at low temperatures and show partial mislocalization of nuclear antigens. Ref.1

Caution

According to Ref.6, it is a component of the 26S proteasome.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   LigandDNA-binding
   Molecular functionActivator
   PTMUbl conjugation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processnegative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 20376190. Source: SGD

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

Inferred from mutant phenotype PubMed 11830665PubMed 15178333. Source: SGD

positive regulation of transcription from RNA polymerase II promoter

Inferred from direct assay Ref.7PubMed 19914394. Source: SGD

positive regulation of transcription from RNA polymerase II promoter in response to stress

Inferred from mutant phenotype PubMed 11027285PubMed 16556235PubMed 18086556PubMed 18627600. Source: SGD

regulation of DNA repair

Inferred from mutant phenotype PubMed 11027285PubMed 20376190. Source: SGD

   Cellular_componentnucleus

Inferred from direct assay PubMed 19914394Ref.1. Source: SGD

   Molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding

Inferred from direct assay Ref.7. Source: SGD

RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription

Inferred from direct assay Ref.7. Source: SGD

metal ion binding

Inferred from electronic annotation. Source: InterPro

protein binding

Inferred from physical interaction Ref.9Ref.10. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MUB1Q031623EBI-15931,EBI-28207
UBR2Q079632EBI-15931,EBI-34338

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 531531Protein RPN4
PRO_0000173871

Regions

Motif382 – 39817Nuclear localization signal Potential
Compositional bias211 – 22919Asp/Glu-rich (acidic)
Compositional bias300 – 31516Asp/Glu-rich (acidic)

Experimental info

Sequence conflict2311C → Y in AAU09680. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Q03465 [UniParc].

Last modified October 1, 1993. Version 1.
Checksum: 4316281AC09FBE7F

FASTA53160,153
        10         20         30         40         50         60 
MASTELSLKR TLTDILEDEL YHTNPGHSQF TSHYQNYHPN ASITPYKLVN KNKENNTFTW 

        70         80         90        100        110        120 
NHSLQHQNES SAASIPPQQT YHFPIFNKYA DPTLTTTTSF TTSEATANDR QINNVHLIPN 

       130        140        150        160        170        180 
EIKGASETPL QKTVNLKNIM KVSDPYVPTR NTFNYDVKIS NDFFDNGDNL YGNDEEVLFY 

       190        200        210        220        230        240 
EDNYNPKMQW SLQDNSAAIN NEDARAIFNN EFDSDDDDIS DDEEDEIEEN CLQQEQHQEE 

       250        260        270        280        290        300 
PLLSLDVTPI SMFGSDQKTG RAKSSSHLFN EYSYVDSNMD SISSVVSEDL LDERGHEKIE 

       310        320        330        340        350        360 
DEDEDNDLDE DDIYDISLLK NRRKQSFVLN KNTIDFERFP SPSTSANVPS TATTGKRKPA 

       370        380        390        400        410        420 
KSSSNRSCVS NSNENGTLER IKKPTSAVVS SNASRRKLIN YTKKHLSSHS STNSNSKPST 

       430        440        450        460        470        480 
ASPSAHTSSS DGNNEIFTCQ IMNLITNEPC GAQFSRSYDL TRHQNTIHAK RKIVFRCSEC 

       490        500        510        520        530 
IKILGSEGYQ KTFSRLDALT RHIKSKHEDL SLEQRQEVTK FAKANIGYVM G 

« Hide

References

« Hide 'large scale' references
[1]"Extragenic suppressors of mutations in the cytoplasmic C-terminus of SEC63 define five genes in Saccharomyces cerevisiae."
Nelson M.K., Kurihara T., Silver P.A.
Genetics 134:159-173(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DISRUPTION PHENOTYPE.
Strain: ATCC 200060 / W303.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"A proteolytic pathway that recognizes ubiquitin as a degradation signal."
Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.
J. Biol. Chem. 270:17442-17456(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
Strain: ATCC 204508 / S288c.
[6]"Son1p is a component of the 26S proteasome of the yeast Saccharomyces cerevisiae."
Fujimuro M., Tanaka K., Yokosawa H., Toh-e A.
FEBS Lett. 423:149-154(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: PRELIMINARY CHARACTERIZATION.
[7]"Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast."
Mannhaupt G., Schnall R., Karpov V., Vetter I., Feldmann H.
FEBS Lett. 450:27-34(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit."
Xie Y., Varshavsky A.
Proc. Natl. Acad. Sci. U.S.A. 98:3056-3061(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase."
Wang L., Mao X., Ju D., Xie Y.
J. Biol. Chem. 279:55218-55223(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION, INTERACTION WITH UBR2.
[10]"Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation."
Ju D., Wang X., Xu H., Xie Y.
Mol. Cell. Biol. 28:1404-1412(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION, INTERACTION WITH MUB1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L00928 Genomic DNA. Translation: AAA35067.1.
Z48432 Genomic DNA. Translation: CAA88339.1.
Z74068 Genomic DNA. Translation: CAA98579.1.
AY723763 Genomic DNA. Translation: AAU09680.1.
BK006938 Genomic DNA. Translation: DAA11830.1.
PIRS41986.
RefSeqNP_010264.3. NM_001180079.3.

3D structure databases

ProteinModelPortalQ03465.
SMRQ03465. Positions 426-508.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32035. 514 interactions.
DIPDIP-5779N.
IntActQ03465. 5 interactions.
MINTMINT-583572.
STRING4932.YDL020C.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDL020C; YDL020C; YDL020C.
GeneID851542.
KEGGsce:YDL020C.

Organism-specific databases

CYGDYDL020c.
SGDS000002178. RPN4.

Phylogenomic databases

eggNOGNOG70197.
HOGENOMHOG000144400.
KOK03034.
OMANKYADPT.
OrthoDBEOG7TF7PD.

Enzyme and pathway databases

BioCycYEAST:G3O-29449-MONOMER.

Gene expression databases

GenevestigatorQ03465.

Family and domain databases

InterProIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
[Graphical view]
SMARTSM00355. ZnF_C2H2. 2 hits.
[Graphical view]
PROSITEPS50157. ZINC_FINGER_C2H2_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio968949.

Entry information

Entry nameRPN4_YEAST
AccessionPrimary (citable) accession number: Q03465
Secondary accession number(s): D6VRX0, E9P944
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: June 11, 2014
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD