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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-382556. ABC-family proteins mediated transport.
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-5689880. Ub-specific processing proteases.
R-SCE-5689901. Metalloprotease DUBs.
R-SCE-6798695. Neutrophil degranulation.
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-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
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)DescriptionActionsGraphical viewLength
Mutagenesisi109H → A: Stabilizes ubiquitin pathway substrates; when associated wirh Ala-111. 1 Publication1
Mutagenesisi111H → A: Stabilizes ubiquitin pathway substrates; when associated wirh Ala-109. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002139601 – 306Ubiquitin carboxyl-terminal hydrolase RPN11Add BLAST306

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionine1 Publication1

Post-translational modificationi

N-acetylated by NAT3.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP43588.
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. 884 interactors.
DIPiDIP-1573N.
IntActiP43588. 26 interactors.
MINTiMINT-405184.

Structurei

Secondary structure

1306
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi26 – 30Combined sources5
Helixi31 – 44Combined sources14
Beta strandi50 – 59Combined sources10
Beta strandi62 – 70Combined sources9
Helixi80 – 82Combined sources3
Helixi85 – 96Combined sources12
Turni97 – 99Combined sources3
Beta strandi103 – 110Combined sources8
Beta strandi112 – 114Combined sources3
Helixi120 – 132Combined sources13
Beta strandi137 – 141Combined sources5
Turni143 – 145Combined sources3
Beta strandi153 – 158Combined sources6
Helixi162 – 166Combined sources5
Helixi182 – 194Combined sources13
Beta strandi195 – 198Combined sources4
Beta strandi200 – 204Combined sources5
Helixi207 – 213Combined sources7
Turni214 – 219Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J47electron microscopy-V230-298[»]
3JCKelectron microscopy3.50G1-306[»]
3JCOelectron microscopy4.80V1-306[»]
3JCPelectron microscopy4.60V1-306[»]
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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi109 – 122JAMMAdd BLAST14

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.
OMAiHENLENT.
OrthoDBiEOG092C3T2O.

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)DescriptionActionsGraphical viewLength
Natural varianti208K → Q in strain: NRRL Y-53. 1
Natural varianti239A → T in strain: NRRL Y-53. 1
Natural varianti262T → S in strain: NRRL Y-53. 1
Natural varianti280 – 281LS → IF in strain: NRRL Y-53. 2

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J47electron microscopy-V230-298[»]
3JCKelectron microscopy3.50G1-306[»]
3JCOelectron microscopy4.80V1-306[»]
3JCPelectron microscopy4.60V1-306[»]
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31152. 884 interactors.
DIPiDIP-1573N.
IntActiP43588. 26 interactors.
MINTiMINT-405184.

Protein family/group databases

MEROPSiM67.001.

PTM databases

iPTMnetiP43588.

Proteomic databases

MaxQBiP43588.
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.
OMAiHENLENT.
OrthoDBiEOG092C3T2O.

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-382556. ABC-family proteins mediated transport.
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-5689880. Ub-specific processing proteases.
R-SCE-5689901. Metalloprotease DUBs.
R-SCE-6798695. Neutrophil degranulation.
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-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
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...

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: November 30, 2016
This is version 152 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.