P25037 (UBP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin carboxyl-terminal hydrolase 1
EC=3.4.19.12

Alternative name(s):
Deubiquitinating enzyme 1
Ubiquitin thioesterase 1
Ubiquitin-specific-processing protease 1

Gene names

Name:	UBP1
Ordered Locus Names:	YDL122W
ORF Names:	D2250

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	809 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.
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).
Miscellaneous	Present with 8970 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 PubMed 1429680Ref.1. Source: SGD ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	endoplasmic reticulum Inferred from direct assay PubMed 15635103. Source: SGD
Molecular_function	ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from direct assay PubMed 1429680. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 809	809	Ubiquitin carboxyl-terminal hydrolase 1		PRO_0000080585
Sites
	Active site	110	1	Nucleophile By similarity
	Active site	697	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	530	1	Phosphoserine Ref.4 Ref.7 Ref.10
	Modified residue	531	1	Phosphoserine Ref.4 Ref.7 Ref.10
	Modified residue	555	1	Phosphoserine Ref.7 Ref.8 Ref.10
	Modified residue	561	1	Phosphotyrosine Ref.10
	Modified residue	618	1	Phosphoserine Ref.7 Ref.8 Ref.9 Ref.10
	Modified residue	638	1	Phosphoserine Ref.7 Ref.10
	Modified residue	670	1	Phosphoserine Ref.7
	Modified residue	672	1	Phosphoserine Ref.6
	Modified residue	755	1	Phosphoserine Ref.7 Ref.10
	Modified residue	776	1	Phosphoserine Ref.9
Experimental info
	Sequence conflict	418	1	L → P in AAA35189. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P25037 [UniParc]. Last modified October 5, 2010. Version 2. Checksum: 07BA266FB43C2C04	FASTA	809	92,769
	10 20 30 40 50 60 MDLFIESKIN SLLQFLFGSR QDFLRNFKTW SNNNNNLSIY LLIFGIVVFF YKKPDHLNYI 70 80 90 100 110 120 VESVSEMTTN FRNNNSLSRW LPRSKFTHLD EEILKRGGFI AGLVNDGNTC FMNSVLQSLA 130 140 150 160 170 180 SSRELMEFLD NNVIRTYEEI EQNEHNEEGN GQESAQDEAT HKKNTRKGGK VYGKHKKKLN 190 200 210 220 230 240 RKSSSKEDEE KSQEPDITFS VALRDLLSAL NAKYYRDKPY FKTNSLLKAM SKSPRKNILL 250 260 270 280 290 300 GYDQEDAQEF FQNILAELES NVKSLNTEKL DTTPVAKSEL PDDALVGQLN LGEVGTVYIP 310 320 330 340 350 360 TEQIDPNSIL HDKSIQNFTP FKLMTPLDGI TAERIGCLQC GENGGIRYSV FSGLSLNLPN 370 380 390 400 410 420 ENIGSTLKLS QLLSDWSKPE IIEGVECNRC ALTAAHSHLF GQLKEFEKKP EGSIPEKLIN 430 440 450 460 470 480 AVKDRVHQIE EVLAKPVIDD EDYKKLHTAN MVRKCSKSKQ ILISRPPPLL SIHINRSVFD 490 500 510 520 530 540 PRTYMIRKNN SKVLFKSRLN LAPWCCDINE INLDARLPMS KKEKAAQQDS SEDENIGGEY 550 560 570 580 590 600 YTKLHERFEQ EFEDSEEEKE YDDAEGNYAS HYNHTKDISN YDPLNGEVDG VTSDDEDEYI 610 620 630 640 650 660 EETDALGNTI KKRIIEHSDV ENENVKDNEE LQEIDNVSLD EPKINVEDQL ETSSDEEDVI 670 680 690 700 710 720 PAPPINYARS FSTVPATPLT YSLRSVIVHY GTHNYGHYIA FRKYRGCWWR ISDETVYVVD 730 740 750 760 770 780 EAEVLSTPGV FMLFYEYDFD EETGKMKDDL EAIQSNNEED DEKEQEQKGV QEPKESQEQG 790 800 EGEEQEEGQE QMKFERTEDH RDISGKDVN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and functional analysis of the ubiquitin-specific protease gene UBP1 of Saccharomyces cerevisiae." Tobias J.W., Varshavsky A. J. Biol. Chem. 266:12021-12028(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530 AND SER-531, MASS SPECTROMETRY. Strain: 2124.
[5]	"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].
[6]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-672, MASS SPECTROMETRY. Strain: YAL6B.
[7]	"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-530; SER-531; SER-555; SER-618; SER-638; SER-670 AND SER-755, MASS SPECTROMETRY. Strain: ADR376.
[8]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-555 AND SER-618, MASS SPECTROMETRY.
[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 SER-618 AND SER-776, 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 SER-530; SER-531; SER-555; TYR-561; SER-618; SER-638 AND SER-755, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M63484 Genomic DNA. Translation: AAA35189.1. Z74170 Genomic DNA. Translation: CAA98690.1. BK006938 Genomic DNA. Translation: DAA11738.1.
PIR	S67665.
RefSeq	NP_010161.1. NM_001180181.1.
3D structure databases
ProteinModelPortal	P25037.
SMR	P25037. Positions 657-735.
ModBase	Search...
Protein-protein interaction databases
IntAct	P25037. 23 interactions.
MINT	MINT-2788387.
STRING	4932.YDL122W.
Protein family/group databases
MEROPS	C19.002.
Proteomic databases
PaxDb	P25037.
PeptideAtlas	P25037.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDL122W; YDL122W; YDL122W.
GeneID	851435.
KEGG	sce:YDL122W.
Organism-specific databases
SGD	S000002280. UBP1.
Phylogenomic databases
eggNOG	NOG259866.
GeneTree	ENSGT00550000075075.
HOGENOM	HOG000093934.
KO	K11870.
OMA	THNYGHY.
OrthoDB	EOG4N33XH.
Enzyme and pathway databases
BioCyc	YEAST:G3O-29521-MONOMER.
Gene expression databases
Genevestigator	P25037.
GermOnline	YDL122W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. [Graphical view]
Pfam	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	968666.

Entry information

Entry name

UBP1_YEAST

Accession

Primary (citable) accession number: P25037
Secondary accession number(s): D6VRM8, Q07543

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	October 5, 2010
Last modified:	May 29, 2013
This is version 116 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program