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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: -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

Miscellaneous

Present with 16400 molecules/cell in log phase SD medium.1 Publication

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).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi109Zinc; catalyticPROSITE-ProRule annotation1
Metal bindingi111Zinc; catalyticPROSITE-ProRule annotation1
Metal bindingi122Zinc; catalyticPROSITE-ProRule annotation1

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • 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

Keywordsi

Molecular functionHydrolase, Metalloprotease, Protease, Thiol protease
Biological processUbl conjugation pathway
LigandMetal-binding, Zinc

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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiP43588
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

Show more details

Protein-protein interaction databases

BioGridi31152, 1221 interactors
DIPiDIP-1573N
IntActiP43588, 51 interactors
MINTiP43588
STRINGi4932.YFR004W

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
Beta strandi72 – 76Combined sources5
Helixi80 – 82Combined sources3
Helixi85 – 97Combined sources13
Beta strandi103 – 110Combined sources8
Turni112 – 114Combined sources3
Helixi120 – 132Combined sources13
Beta strandi137 – 142Combined sources6
Helixi145 – 148Combined sources4
Beta strandi152 – 158Combined sources7
Helixi162 – 166Combined sources5
Helixi182 – 194Combined sources13
Beta strandi196 – 204Combined sources9
Helixi207 – 221Combined sources15
Helixi230 – 260Combined sources31
Helixi263 – 270Combined sources8
Helixi276 – 305Combined sources30

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[»]
5MPBelectron microscopy7.80V1-306[»]
5MPCelectron microscopy7.70V1-306[»]
5MPDelectron microscopy4.10V1-306[»]
5MPEelectron microscopy4.50V1-306[»]
5U4PX-ray2.50B2-219[»]
5W83X-ray1.55B1-222[»]
5WVIelectron microscopy6.30V1-306[»]
5WVKelectron microscopy4.20V1-306[»]
ProteinModelPortaliP43588
SMRiP43588
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini27 – 162MPNPROSITE-ProRule annotationAdd BLAST136

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi109 – 122JAMM motifPROSITE-ProRule annotationAdd 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

Phylogenomic databases

GeneTreeiENSGT00730000111116
HOGENOMiHOG000183690
InParanoidiP43588
KOiK03030
OMAiQTGRPET
OrthoDBiEOG092C3T2O

Family and domain databases

InterProiView protein in InterPro
IPR000555 JAMM/MPN+_dom
IPR037518 MPN
IPR024969 Rpn11/EIF3F_C
PfamiView protein in Pfam
PF01398 JAB, 1 hit
PF13012 MitMem_reg, 1 hit
SMARTiView protein in SMART
SM00232 JAB_MPN, 1 hit
PROSITEiView protein in PROSITE
PS50249 MPN, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiRPN11_YEAST
AccessioniPrimary (citable) accession number: P43588
Secondary accession number(s): D6VTN4, Q8J0T5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: March 28, 2018
This is version 166 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health