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Protein

Ubiquitin carboxyl-terminal hydrolase RPN11

Gene

RPN11

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

Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. RPN11 is the only catalytically active member of the lid and serves as the essential deubiquitinase of the proteasome.3 Publications

Catalytic activityi

Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

GO - Molecular functioni

  • metallopeptidase activity Source: SGD
  • thiol-dependent ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  • mitochondrial fission Source: SGD
  • peroxisome fission Source: SGD
  • proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD
  • proteasome storage granule assembly Source: SGD
  • protein deubiquitination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-30457-MONOMER.
ReactomeiR-SCE-1236978. Cross-presentation of soluble exogenous antigens (endosomes).
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-5668541. TNFR2 non-canonical NF-kB pathway.
R-SCE-5687128. MAPK6/MAPK4 signaling.
R-SCE-68949. Orc1 removal from chromatin.
R-SCE-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-SCE-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-SCE-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Protein family/group databases

MEROPSiM67.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase RPN11 (EC:3.4.19.12)
Alternative name(s):
26S proteasome regulatory subunit RPN11
Protein MPR1
Gene namesi
Name:RPN11
Synonyms:MPR1
Ordered Locus Names:YFR004W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VI

Organism-specific databases

EuPathDBiFungiDB:YFR004W.
SGDiS000001900. RPN11.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrion Source: SGD
  • nucleus Source: SGD
  • proteasome regulatory particle, lid subcomplex Source: SGD
  • proteasome storage granule Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Proteasome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi109 – 1091H → A: Stabilizes ubiquitin pathway substrates; when associated wirh Ala-111. 1 Publication
Mutagenesisi111 – 1111H → A: Stabilizes ubiquitin pathway substrates; when associated wirh Ala-109. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 306306Ubiquitin carboxyl-terminal hydrolase RPN11PRO_0000213960Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine1 Publication

Post-translational modificationi

N-acetylated by NAT3.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP43588.
PeptideAtlasiP43588.
PRIDEiP43588.

PTM databases

iPTMnetiP43588.

Interactioni

Subunit structurei

Component of the lid subcomplex of the 19S proteasome regulatory particle complex (also named PA700 complex). The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. Interacts directly with RPN8 and STS1.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RPN5Q122507EBI-11219,EBI-15935
RPN8Q087237EBI-11219,EBI-36176
RPN9Q040624EBI-11219,EBI-15944

Protein-protein interaction databases

BioGridi31152. 883 interactions.
DIPiDIP-1573N.
IntActiP43588. 26 interactions.
MINTiMINT-405184.

Structurei

Secondary structure

1
306
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi26 – 305Combined sources
Helixi31 – 4414Combined sources
Beta strandi50 – 5910Combined sources
Beta strandi62 – 709Combined sources
Helixi80 – 823Combined sources
Helixi85 – 9612Combined sources
Turni97 – 993Combined sources
Beta strandi103 – 1108Combined sources
Beta strandi112 – 1143Combined sources
Helixi120 – 13213Combined sources
Beta strandi137 – 1415Combined sources
Turni143 – 1453Combined sources
Beta strandi153 – 1586Combined sources
Helixi162 – 1665Combined sources
Helixi182 – 19413Combined sources
Beta strandi195 – 1984Combined sources
Beta strandi200 – 2045Combined sources
Helixi207 – 2137Combined sources
Turni214 – 2196Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J47electron microscopy-V230-298[»]
3JCKelectron microscopy3.50G1-306[»]
4CR2electron microscopy7.70V1-306[»]
4CR3electron microscopy9.30V1-306[»]
4CR4electron microscopy8.80V1-306[»]
4O8XX-ray1.99B2-239[»]
4O8YX-ray1.95B2-239[»]
4OCLX-ray2.40B/E1-220[»]
4OCMX-ray1.99B/E1-220[»]
4OCNX-ray2.25B/E1-220[»]
4OWPX-ray2.35B2-229[»]
5A5Belectron microscopy9.50V1-306[»]
ProteinModelPortaliP43588.
SMRiP43588. Positions 23-298.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi109 – 12214JAMMAdd
BLAST

Domaini

The JAMM motif is required for the deubiquitination and degradation of ubiquitinated substrates.1 Publication

Sequence similaritiesi

Belongs to the peptidase M67A family.Curated
Contains 1 MPN (JAB/Mov34) domain.Curated

Phylogenomic databases

GeneTreeiENSGT00730000111116.
HOGENOMiHOG000183690.
InParanoidiP43588.
KOiK03030.
OMAiTQQSFES.
OrthoDBiEOG7RV9S0.

Family and domain databases

InterProiIPR000555. JAMM/MPN+_dom.
IPR024969. Rpn11/EIF3F_C.
[Graphical view]
PfamiPF01398. JAB. 1 hit.
PF13012. MitMem_reg. 1 hit.
[Graphical view]
SMARTiSM00232. JAB_MPN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43588-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERLQRLMMN SKVGSADTGR DDTKETVYIS SIALLKMLKH GRAGVPMEVM
60 70 80 90 100
GLMLGEFVDD YTVNVVDVFA MPQSGTGVSV EAVDDVFQAK MMDMLKQTGR
110 120 130 140 150
DQMVVGWYHS HPGFGCWLSS VDVNTQKSFE QLNSRAVAVV VDPIQSVKGK
160 170 180 190 200
VVIDAFRLID TGALINNLEP RQTTSNTGLL NKANIQALIH GLNRHYYSLN
210 220 230 240 250
IDYHKTAKET KMLMNLHKEQ WQSGLKMYDY EEKEESNLAA TKSMVKIAEQ
260 270 280 290 300
YSKRIEEEKE LTEEELKTRY VGRQDPKKHL SETADETLEN NIVSVLTAGV

NSVAIK
Length:306
Mass (Da):34,398
Last modified:November 1, 1995 - v1
Checksum:i9DDE8BD74890894D
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti208 – 2081K → Q in strain: NRRL Y-53.
Natural varianti239 – 2391A → T in strain: NRRL Y-53.
Natural varianti262 – 2621T → S in strain: NRRL Y-53.
Natural varianti280 – 2812LS → IF in strain: NRRL Y-53.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79561 Genomic DNA. Translation: CAA56098.1.
AY152546 Genomic DNA. Translation: AAN77865.1.
D50617 Genomic DNA. Translation: BAA09243.1.
AY692755 Genomic DNA. Translation: AAT92774.1.
BK006940 Genomic DNA. Translation: DAA12444.1.
PIRiS56259.
RefSeqiNP_116659.1. NM_001179969.1.

Genome annotation databases

EnsemblFungiiBAA09243; BAA09243; BAA09243.
YFR004W; YFR004W; YFR004W.
GeneIDi850554.
KEGGisce:YFR004W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79561 Genomic DNA. Translation: CAA56098.1.
AY152546 Genomic DNA. Translation: AAN77865.1.
D50617 Genomic DNA. Translation: BAA09243.1.
AY692755 Genomic DNA. Translation: AAT92774.1.
BK006940 Genomic DNA. Translation: DAA12444.1.
PIRiS56259.
RefSeqiNP_116659.1. NM_001179969.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J47electron microscopy-V230-298[»]
3JCKelectron microscopy3.50G1-306[»]
4CR2electron microscopy7.70V1-306[»]
4CR3electron microscopy9.30V1-306[»]
4CR4electron microscopy8.80V1-306[»]
4O8XX-ray1.99B2-239[»]
4O8YX-ray1.95B2-239[»]
4OCLX-ray2.40B/E1-220[»]
4OCMX-ray1.99B/E1-220[»]
4OCNX-ray2.25B/E1-220[»]
4OWPX-ray2.35B2-229[»]
5A5Belectron microscopy9.50V1-306[»]
ProteinModelPortaliP43588.
SMRiP43588. Positions 23-298.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31152. 883 interactions.
DIPiDIP-1573N.
IntActiP43588. 26 interactions.
MINTiMINT-405184.

Protein family/group databases

MEROPSiM67.001.

PTM databases

iPTMnetiP43588.

Proteomic databases

MaxQBiP43588.
PeptideAtlasiP43588.
PRIDEiP43588.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiBAA09243; BAA09243; BAA09243.
YFR004W; YFR004W; YFR004W.
GeneIDi850554.
KEGGisce:YFR004W.

Organism-specific databases

EuPathDBiFungiDB:YFR004W.
SGDiS000001900. RPN11.

Phylogenomic databases

GeneTreeiENSGT00730000111116.
HOGENOMiHOG000183690.
InParanoidiP43588.
KOiK03030.
OMAiTQQSFES.
OrthoDBiEOG7RV9S0.

Enzyme and pathway databases

BioCyciYEAST:G3O-30457-MONOMER.
ReactomeiR-SCE-1236978. Cross-presentation of soluble exogenous antigens (endosomes).
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-5668541. TNFR2 non-canonical NF-kB pathway.
R-SCE-5687128. MAPK6/MAPK4 signaling.
R-SCE-68949. Orc1 removal from chromatin.
R-SCE-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-SCE-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-SCE-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

PROiP43588.

Family and domain databases

InterProiIPR000555. JAMM/MPN+_dom.
IPR024969. Rpn11/EIF3F_C.
[Graphical view]
PfamiPF01398. JAB. 1 hit.
PF13012. MitMem_reg. 1 hit.
[Graphical view]
SMARTiSM00232. JAB_MPN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A Saccharomyces cerevisiae gene essential for viability has been conserved in evolution."
    Rinaldi T., Bolotin-Fukuhara M., Frontali L.
    Gene 160:135-136(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: S288c / GRF88.
  2. "A putative naturally occurring allele of RPN11."
    Ambroggio X.I., Rees D.C., Deshaies R.J.
    Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 2601 / CBS 679 / DSM 3774 / NRRL Y-53.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. "N-terminal modifications of the 19S regulatory particle subunits of the yeast proteasome."
    Kimura Y., Saeki Y., Yokosawa H., Polevoda B., Sherman F., Hirano H.
    Arch. Biochem. Biophys. 409:341-348(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-8, ACETYLATION AT MET-1.
  7. "Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome."
    Verma R., Aravind L., Oania R., McDonald W.H., Yates J.R., Koonin E.V., Deshaies R.J.
    Science 298:611-615(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF HIS-109 AND HIS-111.
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. Cited for: FUNCTION, INTERACTION WITH STS1.
  10. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (7.4 ANGSTROMS) OF THE 26S PROTEASOME.
  11. "Structure of the 26S proteasome with ATP-gammaS bound provides insights into the mechanism of nucleotide-dependent substrate translocation."
    Sledz P., Unverdorben P., Beck F., Pfeifer G., Schweitzer A., Forster F., Baumeister W.
    Proc. Natl. Acad. Sci. U.S.A. 110:7264-7269(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (9.80 ANGSTROMS), IDENTIFICATION IN THE 26S PROTEASOME COMPLEX.
  12. "Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid."
    Estrin E., Lopez-Blanco J.R., Chacon P., Martin A.
    Structure 21:1624-1635(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (9.80 ANGSTROMS), IDENTIFICATION IN THE 26S PROTEASOME COMPLEX.
  13. "Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation."
    Worden E.J., Padovani C., Martin A.
    Nat. Struct. Mol. Biol. 21:220-227(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 2-239 IN COMPLEX WITH RPN8, FUNCTION.

Entry informationi

Entry nameiRPN11_YEAST
AccessioniPrimary (citable) accession number: P43588
Secondary accession number(s): D6VTN4, Q8J0T5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: June 8, 2016
This is version 147 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 16400 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: 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.