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Protein

Ubiquitin carboxyl-terminal hydrolase 2

Gene

UBP2

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

Has an ATP-independent isopeptidase activity, cleaving at the C-terminus of the ubiquitin moiety in natural or engineered linear fusion proteins, irrespective of their size or the presence of an N-terminal extension to ubiquitin. Removes ubiquitin chains that initiate proteolysis of FZO1 and inhibit mitochondrial fusion.2 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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei745 – 7451NucleophilePROSITE-ProRule annotation
Active sitei1209 – 12091Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  1. protein deubiquitination Source: SGD
  2. ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Source: SGD
  3. ubiquitin homeostasis Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-33651-MONOMER.

Protein family/group databases

MEROPSiC19.003.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 2 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 2
Ubiquitin thioesterase 2
Ubiquitin-specific-processing protease 2
Gene namesi
Name:UBP2
Ordered Locus Names:YOR124C
ORF Names:O3281, YOR3281C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XV

Organism-specific databases

CYGDiYOR124c.
EuPathDBiFungiDB:YOR124C.
SGDiS000005650. UBP2.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12721272Ubiquitin carboxyl-terminal hydrolase 2PRO_0000080586Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei907 – 9071Phosphoserine3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ01476.
PaxDbiQ01476.
PeptideAtlasiQ01476.

Expressioni

Gene expression databases

GenevestigatoriQ01476.

Interactioni

Subunit structurei

Forms a ternary complex with RSP5 and RUP1. Interacts with FZO1.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RUP1Q122423EBI-19826,EBI-38794

Protein-protein interaction databases

BioGridi34519. 85 interactions.
DIPiDIP-2647N.
IntActiQ01476. 10 interactions.
MINTiMINT-427685.
STRINGi4932.YOR124C.

Structurei

3D structure databases

ProteinModelPortaliQ01476.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini736 – 1258523USPAdd
BLAST

Sequence similaritiesi

Belongs to the peptidase C19 family.Curated
Contains 1 USP domain.Curated

Phylogenomic databases

eggNOGiNOG275561.
HOGENOMiHOG000094458.
InParanoidiQ01476.
KOiK11849.
OMAiHRGEASY.
OrthoDBiEOG7327X3.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR025305. UCH_repeat_domain.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF13446. RPT. 2 hits.
PF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q01476-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPNEDNELQK AIENHHNQLL NQDKENADRN GSVIEDLPLY GTSINQQSTP
60 70 80 90 100
GDVDDGKHLL YPDIATNLPL KTSDRLLDDI LCDTIFLNST DPKVMQKGLQ
110 120 130 140 150
SRGILKESML SYSTFRSSIR PNCLGSLTDQ VVFQTKSEYD SISCPKYNKI
160 170 180 190 200
HVFQAVIFNP SLAEQQISTF DDIVKIPIYH LKVSVKVRQE LERLKKHVGV
210 220 230 240 250
TQFHSLDHLH EYDRVDLSTF DSSDPNLLDY GIYVSDDTNK LILIEIFKPE
260 270 280 290 300
FNSPEEHESF TADAIKKRYN AMCVKNESLD KSETPSQVDC FYTLFKIFKG
310 320 330 340 350
PLTRKSKAEP TKTIDSGNLA LNTHLNPEWL TSKYGFQASS EIDEETNEIF
360 370 380 390 400
TEYVPPDMVD YVNDLETRKI RESFVRKCLQ LIFWGQLSTS LLAPNSPLKN
410 420 430 440 450
TKSVKGMSSL QTSFSTLPWF HLLGESRARI LLNSNEQTHS PLDAEPHFIN
460 470 480 490 500
LSVSHYYTDR DIIRNYESLS SLDPENIGLY FDALTYIANR KGAYQLIAYC
510 520 530 540 550
GKQDIIGQEA LENALLMFKI NPKECNISEL NEATLLSIYK YETSNKSQVT
560 570 580 590 600
SNHLTNLKNA LRLLAKYTKS DKLKFYVDHE PYRALSQAYD TLSIDESVDE
610 620 630 640 650
DIIKTAYSVK INDSPGLKLD CDRALYTIAI SKRSLDLFNF LTEECPQFSN
660 670 680 690 700
YYGPEKLDYQ EALKLLQVNE NASDETILKI FKQKWFDENV YEPDQFLILR
710 720 730 740 750
AALTKISIER NSTLITNFLL TGTIDPNSLP PENWPTGINN IGNTCYLNSL
760 770 780 790 800
LQYYFSIAPL RRYVLEYQKT VENFNDHLSN SGHIRRIGGR EISRGEVERS
810 820 830 840 850
IQFIYQLRNL FYAMVHTRER CVTPSKELAY LAFAPSNVEV EFEVEGNKVV
860 870 880 890 900
DQTGVLSDSK KETTDDAFTT KIKDTSLIDL EMEDGLNGDV GTDANRKKNE
910 920 930 940 950
SNDAEVSENE DTTGLTSPTR VAKISSDQLE NALEMGRQQD VTECIGNVLF
960 970 980 990 1000
QIESGSEPIR YDEDNEQYDL VKQLFYGTTK QSIVPLSATN KVRTKVERFL
1010 1020 1030 1040 1050
SLLINIGDHP KDIYDAFDSY FKDEYLTMEE YGDVIRTVAV TTFPTILQVQ
1060 1070 1080 1090 1100
IQRVYYDRER LMPFKSIEPL PFKEVIYMDR YADTENPLLL AKKKETEEMK
1110 1120 1130 1140 1150
QKLKVMKNRQ RELLSRDDSG LTRKDAFLES IKLLESDTIK KTPLKIEAAN
1160 1170 1180 1190 1200
DVIKTLRNNV QNIDNELMKL YNDINSLEEK ISHQFDDFKE YGYSLFSVFI
1210 1220 1230 1240 1250
HRGEASYGHY WIYIKDRNRN GIWRKYNDET ISEVQEEEVF NFNEGNTATP
1260 1270
YFLVYVKQGQ EGDIEPLKRI LK
Length:1,272
Mass (Da):146,355
Last modified:November 1, 1997 - v2
Checksum:i6D106539AE5C5F3F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti658 – 6658Missing (PubMed:1429680).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M94916 Genomic DNA. Translation: AAA35190.1.
X94335 Genomic DNA. Translation: CAA64043.1.
X90518 Genomic DNA. Translation: CAA62120.1.
Z75032 Genomic DNA. Translation: CAA99323.1.
BK006948 Genomic DNA. Translation: DAA10898.1.
PIRiS60999.
RefSeqiNP_014767.3. NM_001183543.3.

Genome annotation databases

EnsemblFungiiYOR124C; YOR124C; YOR124C.
GeneIDi854291.
KEGGisce:YOR124C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M94916 Genomic DNA. Translation: AAA35190.1.
X94335 Genomic DNA. Translation: CAA64043.1.
X90518 Genomic DNA. Translation: CAA62120.1.
Z75032 Genomic DNA. Translation: CAA99323.1.
BK006948 Genomic DNA. Translation: DAA10898.1.
PIRiS60999.
RefSeqiNP_014767.3. NM_001183543.3.

3D structure databases

ProteinModelPortaliQ01476.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34519. 85 interactions.
DIPiDIP-2647N.
IntActiQ01476. 10 interactions.
MINTiMINT-427685.
STRINGi4932.YOR124C.

Protein family/group databases

MEROPSiC19.003.

Proteomic databases

MaxQBiQ01476.
PaxDbiQ01476.
PeptideAtlasiQ01476.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR124C; YOR124C; YOR124C.
GeneIDi854291.
KEGGisce:YOR124C.

Organism-specific databases

CYGDiYOR124c.
EuPathDBiFungiDB:YOR124C.
SGDiS000005650. UBP2.

Phylogenomic databases

eggNOGiNOG275561.
HOGENOMiHOG000094458.
InParanoidiQ01476.
KOiK11849.
OMAiHRGEASY.
OrthoDBiEOG7327X3.

Enzyme and pathway databases

BioCyciYEAST:G3O-33651-MONOMER.

Miscellaneous databases

NextBioi976278.
PROiQ01476.

Gene expression databases

GenevestigatoriQ01476.

Family and domain databases

InterProiIPR001394. Peptidase_C19_UCH.
IPR025305. UCH_repeat_domain.
IPR018200. USP_CS.
IPR028889. USP_dom.
[Graphical view]
PfamiPF13446. RPT. 2 hits.
PF00443. UCH. 1 hit.
[Graphical view]
PROSITEiPS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family."
    Baker R.T., Tobias J.W., Varshavsky A.
    J. Biol. Chem. 267:23364-23375(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequencing and analysis of 51 kb on the right arm of chromosome XV from Saccharomyces cerevisiae reveals 30 open reading frames."
    Wiemann S., Rechmann S., Benes V., Voss H., Schwager C., Vlcek C., Stegemann J., Zimmermann J., Erfle H., Paces V., Ansorge W.
    Yeast 12:281-288(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  7. "The Rsp5 ubiquitin ligase is coupled to and antagonized by the Ubp2 deubiquitinating enzyme."
    Kee Y., Lyon N., Huibregtse J.M.
    EMBO J. 24:2414-2424(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RSP5 AND RUP1.
  8. "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-907, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  9. "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-907, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "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-907, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Two deubiquitylases act on mitofusin and regulate mitochondrial fusion along independent pathways."
    Anton F., Dittmar G., Langer T., Escobar-Henriques M.
    Mol. Cell 49:487-498(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DEUBIQUITINATION OF FZO1, INTERACTION WITH FZO1.

Entry informationi

Entry nameiUBP2_YEAST
AccessioniPrimary (citable) accession number: Q01476
Secondary accession number(s): D6W2I2, Q99357
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: April 29, 2015
This is version 137 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2420 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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 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.