Q01476 (UBP2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	UBP2
Ordered Locus Names:	YOR124C
ORF Names:	O3281, YOR3281C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1272 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.11
Catalytic activity	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).
Subunit structure	Forms a ternary complex with RSP5 and RUP1. Interacts with FZO1. Ref.7 Ref.11
Miscellaneous	Present with 2420 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase C19 family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein deubiquitination Inferred from direct assay Ref.7. Source: SGD ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Inferred from physical interaction PubMed 19165343. Source: SGD
Cellular_component	cytoplasm Inferred by curator Ref.1. Source: SGD
Molecular_function	ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from direct assay Ref.1. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RUP1	Q12242	3	EBI-19826,EBI-38794

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1272	1272	Ubiquitin carboxyl-terminal hydrolase 2		PRO_0000080586
Sites
	Active site	745	1	Nucleophile By similarity
	Active site	1209	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	875	1	Phosphothreonine Ref.9 Ref.10
	Modified residue	876	1	Phosphoserine Ref.10
	Modified residue	907	1	Phosphoserine Ref.8 Ref.9 Ref.10
Experimental info
	Sequence conflict	658 – 665	8	Missing Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q01476 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 6D106539AE5C5F3F	FASTA	1,272	146,355
	10 20 30 40 50 60 MPNEDNELQK AIENHHNQLL NQDKENADRN GSVIEDLPLY GTSINQQSTP GDVDDGKHLL 70 80 90 100 110 120 YPDIATNLPL KTSDRLLDDI LCDTIFLNST DPKVMQKGLQ SRGILKESML SYSTFRSSIR 130 140 150 160 170 180 PNCLGSLTDQ VVFQTKSEYD SISCPKYNKI HVFQAVIFNP SLAEQQISTF DDIVKIPIYH 190 200 210 220 230 240 LKVSVKVRQE LERLKKHVGV TQFHSLDHLH EYDRVDLSTF DSSDPNLLDY GIYVSDDTNK 250 260 270 280 290 300 LILIEIFKPE FNSPEEHESF TADAIKKRYN AMCVKNESLD KSETPSQVDC FYTLFKIFKG 310 320 330 340 350 360 PLTRKSKAEP TKTIDSGNLA LNTHLNPEWL TSKYGFQASS EIDEETNEIF TEYVPPDMVD 370 380 390 400 410 420 YVNDLETRKI RESFVRKCLQ LIFWGQLSTS LLAPNSPLKN TKSVKGMSSL QTSFSTLPWF 430 440 450 460 470 480 HLLGESRARI LLNSNEQTHS PLDAEPHFIN LSVSHYYTDR DIIRNYESLS SLDPENIGLY 490 500 510 520 530 540 FDALTYIANR KGAYQLIAYC GKQDIIGQEA LENALLMFKI NPKECNISEL NEATLLSIYK 550 560 570 580 590 600 YETSNKSQVT SNHLTNLKNA LRLLAKYTKS DKLKFYVDHE PYRALSQAYD TLSIDESVDE 610 620 630 640 650 660 DIIKTAYSVK INDSPGLKLD CDRALYTIAI SKRSLDLFNF LTEECPQFSN YYGPEKLDYQ 670 680 690 700 710 720 EALKLLQVNE NASDETILKI FKQKWFDENV YEPDQFLILR AALTKISIER NSTLITNFLL 730 740 750 760 770 780 TGTIDPNSLP PENWPTGINN IGNTCYLNSL LQYYFSIAPL RRYVLEYQKT VENFNDHLSN 790 800 810 820 830 840 SGHIRRIGGR EISRGEVERS IQFIYQLRNL FYAMVHTRER CVTPSKELAY LAFAPSNVEV 850 860 870 880 890 900 EFEVEGNKVV DQTGVLSDSK KETTDDAFTT KIKDTSLIDL EMEDGLNGDV GTDANRKKNE 910 920 930 940 950 960 SNDAEVSENE DTTGLTSPTR VAKISSDQLE NALEMGRQQD VTECIGNVLF QIESGSEPIR 970 980 990 1000 1010 1020 YDEDNEQYDL VKQLFYGTTK QSIVPLSATN KVRTKVERFL SLLINIGDHP KDIYDAFDSY 1030 1040 1050 1060 1070 1080 FKDEYLTMEE YGDVIRTVAV TTFPTILQVQ IQRVYYDRER LMPFKSIEPL PFKEVIYMDR 1090 1100 1110 1120 1130 1140 YADTENPLLL AKKKETEEMK QKLKVMKNRQ RELLSRDDSG LTRKDAFLES IKLLESDTIK 1150 1160 1170 1180 1190 1200 KTPLKIEAAN DVIKTLRNNV QNIDNELMKL YNDINSLEEK ISHQFDDFKE YGYSLFSVFI 1210 1220 1230 1240 1250 1260 HRGEASYGHY WIYIKDRNRN GIWRKYNDET ISEVQEEEVF NFNEGNTATP YFLVYVKQGQ 1270 EGDIEPLKRI LK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"DNA sequencing and analysis of 130 kb from yeast chromosome XV." Voss H., Benes V., Andrade M.A., Valencia A., Rechmann S., Teodoru C., Schwager C., Paces V., Sander C., Ansorge W. Yeast 13:655-672(1997) [PubMed] [Europe PMC] [Abstract] 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 96604 / S288c / FY1679.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] 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, MASS SPECTROMETRY. Strain: ADR376.
[9]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-875 AND SER-907, MASS SPECTROMETRY.
[10]	"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 THR-875; SER-876 AND SER-907, MASS SPECTROMETRY.
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	S60999.
RefSeq	NP_014767.3. NM_001183543.3.
3D structure databases
ProteinModelPortal	Q01476.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2647N.
IntAct	Q01476. 8 interactions.
MINT	MINT-427685.
STRING	4932.YOR124C.
Protein family/group databases
MEROPS	C19.003.
Proteomic databases
PaxDb	Q01476.
PeptideAtlas	Q01476.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YOR124C; YOR124C; YOR124C.
GeneID	854291.
KEGG	sce:YOR124C. sce:YOR126C.
Organism-specific databases
CYGD	YOR124c.
SGD	S000005650. UBP2.
Phylogenomic databases
eggNOG	NOG275561.
GeneTree	ENSGT00390000016082.
HOGENOM	HOG000094458.
KO	K01175. K11849.
OMA	GINNIGN.
OrthoDB	EOG498Z7X.
Gene expression databases
Genevestigator	Q01476.
GermOnline	YOR124C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. IPR025305. UCH_repeat_domain. [Graphical view]
Pfam	PF13446. RPT. 2 hits. PF00443. UCH. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	976278.

Entry information

Entry name

UBP2_YEAST

Accession

Primary (citable) accession number: Q01476
Secondary accession number(s): D6W2I2, Q99357

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	November 1, 1997
Last modified:	April 3, 2013
This is version 119 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program