Ubiquitin carboxyl-terminal hydrolase 4 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P32571 (UBP4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified November 13, 2013. Version 142. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ubiquitin carboxyl-terminal hydrolase 4
EC=3.4.19.12

Alternative name(s):
Deubiquitinating enzyme 4
Ubiquitin thioesterase 4
Ubiquitin-specific-processing protease 4
Vacuole biogenesis protein SSV7

Gene names

Name:	DOA4
Synonyms:	DOS1, MUT4, NPI2, SSV7, UBP4
Ordered Locus Names:	YDR069C
ORF Names:	D4270, YD8554.02C, YD9609.23C

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	926 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin thioesterase that acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins en route to the vacuole. Removes also ubiquitin from soluble proteins targeted to proteasomes. Is essential to maintain a normal level of free ubiquitin. Involved in the ammonium-induced down-regulation of the GAP1 permease and the UME3 destruction in response to oxidative stress. Has a role in the RAD9 checkpoint response to TOP1 poisons. Required for promoting coordination of DNA replication and avoids DNA overreplication. Ref.1 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18 Ref.21 Ref.22 Ref.25 Ref.26 Ref.27 Ref.29
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).
Enzyme regulation	RFU1 is an inhibitor of deubiquitination activity. Ref.31
Subunit structure	Interacts with BRO1, RFU1 and VPS32. Associates with the 26S proteasome. Ref.22 Ref.23 Ref.27 Ref.28 Ref.31
Subcellular location	Cytoplasm. Late endosome membrane; Peripheral membrane protein. Note: Recruited to the late endosome by BRO1. Ref.14 Ref.19 Ref.22 Ref.24 Ref.25 Ref.27 Ref.28
Domain	Residues 1-208 are essential for the localization to the late endosome and constitute a late endosome localization (LEL) domain. Ref.25
Miscellaneous	Present with 428 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase C19 family. Contains 1 rhodanese domain.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm Endosome Membrane
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	endocytosis Inferred from mutant phenotype Ref.8. Source: SGD free ubiquitin chain depolymerization Inferred from direct assay Ref.31. Source: SGD intralumenal vesicle formation Inferred from genetic interaction PubMed 23444383. Source: SGD regulation of DNA replication Inferred from mutant phenotype Ref.6. Source: SGD ubiquitin homeostasis Inferred from mutant phenotype Ref.31. Source: SGD ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Inferred from mutant phenotype Ref.29. Source: SGD
Cellular_component	endosome Inferred from direct assay Ref.25. Source: SGD late endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell proteasome complex Inferred from physical interaction Ref.11. Source: SGD
Molecular_function	endopeptidase activity Inferred from genetic interaction Ref.11. Source: SGD ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from direct assay Ref.31 Ref.1. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BRO1	P48582	15	EBI-19840,EBI-3768
RFU1	Q08003	2	EBI-19840,EBI-2353109

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 926

926

Ubiquitin carboxyl-terminal hydrolase 4

PRO_0000080589

Regions

Domain

205 – 328

124

Rhodanese

Compositional bias

386 – 392

Poly-Gln

Sites

Active site

571

Nucleophile

Active site

880

Proton acceptor By similarity

Amino acid modifications

Modified residue

443

Phosphoserine Ref.30

Experimental info

Mutagenesis

571

C → S or A: Impairs deubiquitination activity and protein sorting into the MVB pathway. Ref.27 Ref.29

Mutagenesis

826

Y → A: Impairs deubiquitination activity and binding to BRO1; when associated with A-827 and A-829. Ref.27

Mutagenesis

827

P → A: Impairs deubiquitination activity and binding to BRO1; when associated with A-826 and A-829. Ref.27

Mutagenesis

829

L → A: Impairs deubiquitination activity and binding to BRO1; when associated with A-826 and A-827. Ref.27

Sequence conflict

327

Q → K in AAA35105. Ref.2

Sequence conflict

345

I → F in AAA35105. Ref.2

Sequence conflict

375 – 378

MLVA → TASW in AAA35105. Ref.2

Sequence conflict

383

N → I in AAA35105. Ref.2

Sequence conflict

407

K → T in AAA35105. Ref.2

Sequence conflict

543 – 570

LDHTD…NLGNS → FRSYEMLHQLLLIIMTLISR LVWENLEIP in AAA35105. Ref.2

Sequence conflict

580

I → T in AAA35105. Ref.2

Sequence conflict

836

W → G in AAA35105. Ref.2

Sequence conflict

897

D → N in AAA35105. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P32571 [UniParc].

Last modified February 1, 1994. Version 2.
Checksum: B863FE6062510F3C
Show »

FASTA

926

105,192

        10         20         30         40         50         60 
MEQNIISTIR DECIRHRSKY LTIAQLTAIA EAKINEFIIT GKAKDQDLSS LLDKCIDILS 

        70         80         90        100        110        120 
IYKKNSKDIK NIISCKNKGA MISSNSVMII QLNYVYYKVI HIIVTTNIPH LSEFAKIKLH 

       130        140        150        160        170        180 
KSTSDEGNGN NNNNEFQLMN IYNTLLETLL KDENIAKIKS FIKSSIKQTK LNHEQEECNL 

       190        200        210        220        230        240 
MRTGSYITSN QLNSLISSSA NSASSQMEIL LIDIRSRLEF NKSHIDTKNI ICLEPISFKM 

       250        260        270        280        290        300 
SYSDHDLEKK SLITSPNSEI KMFQSRNLFK FIILYTDANE YNVKQQSVLL DILVNHSFEK 

       310        320        330        340        350        360 
PISDDFTKIF ILESGFPGWL KSNYGRQVSS SFPSNNNIKD DSVYINGNTS GLSLQHLPKM 

       370        380        390        400        410        420 
SPSIRHSMDD SMKEMLVAPT PLNHLQQQQQ QQSDNDHVLK RSSSFKKLFS NYTSPNPKNS 

       430        440        450        460        470        480 
NSNLYSISSL SISSSPSPLP LHSPDPVKGN SLPINYPETP HLWKNSETDF MTNQREQLNH 

       490        500        510        520        530        540 
NSFAHIAPIN TKAITSPSRT ATPKLQRFPQ TISMNLNMNS NGHSSATSTI QPSCLSLSNN 

       550        560        570        580        590        600 
DSLDHTDVTP TSSHNYDLDF AVGLENLGNS CYMNCIIQCI LGTHELTQIF LDDSYAKHIN 

       610        620        630        640        650        660 
INSKLGSKGI LAKYFARLVH MMYKEQVDGS KKISISPIKF KLACGSVNSL FKTASQQDCQ 

       670        680        690        700        710        720 
EFCQFLLDGL HEDLNQCGSN PPLKELSQEA EARREKLSLR IASSIEWERF LTTDFSVIVD 

       730        740        750        760        770        780 
LFQGQYASRL KCKVCSHTST TYQPFTVLSI PIPKKNSRNN ITIEDCFREF TKCENLEVDE 

       790        800        810        820        830        840 
QWLCPHCEKR QPSTKQLTIT RLPRNLIVHL KRFDNLLNKN NDFVIYPFLL DLTPFWANDF 

       850        860        870        880        890        900 
DGVFPPGVND DELPIRGQIP PFKYELYGVA CHFGTLYGGH YTAYVKKGLK KGWLYFDDTK 

       910        920 
YKPVKNKADA INSNAYVLFY HRVYGV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yeast DOA4 gene encodes a deubiquitinating enzyme related to a product of the human tre-2 oncogene." Papa F.R., Hochstrasser M. Nature 366:313-319(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	Latterich M. Submitted (JAN-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"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. Zaccaria P. Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Nucleotide sequence analysis of a 32,500 bp region of the right arm of Saccharomyces cerevisiae chromosome IV." Brandt P., Ramlow S., Otto B., Bloecker H. Yeast 12:85-90(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 36-926. Strain: ATCC 204508 / S288c.
[6]	"Coordinating DNA replication to produce one copy of the genome requires genes that act in ubiquitin metabolism." Singer J.D., Manning B.M., Formosa T. Mol. Cell. Biol. 16:1356-1366(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Ubiquitin lys63 is involved in ubiquitination of a yeast plasma membrane protein." Galan J.-M., Haguenauer-Tsapis R. EMBO J. 16:5847-5854(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Catabolite inactivation of the yeast maltose transporter requires ubiquitin-ligase npi1/rsp5 and ubiquitin-hydrolase npi2/doa4." Lucero P., Lagunas R. FEMS Microbiol. Lett. 147:273-277(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Role for the ubiquitin-proteasome system in the vacuolar degradation of Ste6p, the a-factor transporter in Saccharomyces cerevisiae." Loayza D., Michaelis S. Mol. Cell. Biol. 18:779-789(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"NH4+-induced down-regulation of the Saccharomyces cerevisiae Gap1p permease involves its ubiquitination with lysine-63-linked chains." Springael J.-Y., Galan J.-M., Haguenauer-Tsapis R., Andre B. J. Cell Sci. 112:1375-1383(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Interaction of the Doa4 deubiquitinating enzyme with the yeast 26S proteasome." Papa F.R., Amerik A.Y., Hochstrasser M. Mol. Biol. Cell 10:741-756(1999) [PubMed] [Europe PMC] [Abstract] Cited for: ASSOCIATION WITH THE 26S PROTEASOME.
[12]	"The Doa4 deubiquitinating enzyme is required for ubiquitin homeostasis in yeast." Swaminathan S., Amerik A.Y., Hochstrasser M. Mol. Biol. Cell 10:2583-2594(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"Oxidative stress-induced destruction of the yeast C-type cyclin Ume3p requires phosphatidylinositol-specific phospholipase C and the 26S proteasome." Cooper K.F., Mallory M.J., Strich R. Mol. Cell. Biol. 19:3338-3348(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[14]	"The Doa4 deubiquitinating enzyme is functionally linked to the vacuolar protein-sorting and endocytic pathways." Amerik A.Y., Nowak J., Swaminathan S., Hochstrasser M. Mol. Biol. Cell 11:3365-3380(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[15]	"Glucose-induced monoubiquitination of the Saccharomyces cerevisiae galactose transporter is sufficient to signal its internalization." Horak J., Wolf D.H. J. Bacteriol. 183:3083-3088(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[16]	"Uptake of the ATP-binding cassette (ABC) transporter Ste6 into the yeast vacuole is blocked in the doa4 Mutant." Losko S., Kopp F., Kranz A., Koelling R. Mol. Biol. Cell 12:1047-1059(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[17]	"Deubiquitination step in the endocytic pathway of yeast plasma membrane proteins: crucial role of Doa4p ubiquitin isopeptidase." Dupre S., Haguenauer-Tsapis R. Mol. Cell. Biol. 21:4482-4494(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[18]	"Permease recycling and ubiquitination status reveal a particular role for Bro1 in the multivesicular body pathway." Nikko E., Marini A.-M., Andre B. J. Biol. Chem. 278:50732-50743(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[19]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[20]	"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].
[21]	"The deubiquitinating enzyme Doa4p protects cells from DNA topoisomerase I poisons." Fiorani P., Reid R.J.D., Schepis A., Jacquiau H.R., Guo H., Thimmaiah P., Benedetti P., Bjornsti M.-A. J. Biol. Chem. 279:21271-21281(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[22]	"Bro1 coordinates deubiquitination in the multivesicular body pathway by recruiting Doa4 to endosomes." Luhtala N., Odorizzi G. J. Cell Biol. 166:717-729(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH BRO1.
[23]	"Protein-protein interactions of ESCRT complexes in the yeast Saccharomyces cerevisiae." Bowers K., Lottridge J., Helliwell S.B., Goldthwaite L.M., Luzio J.P., Stevens T.H. Traffic 5:194-210(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH VPS32.
[24]	"Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes." Nickerson D.P., West M., Odorizzi G. J. Cell Biol. 175:715-720(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[25]	"A conserved late endosome-targeting signal required for Doa4 deubiquitylating enzyme function." Amerik A.Y., Sindhi N., Hochstrasser M. J. Cell Biol. 175:825-835(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN.
[26]	"Amino acids regulate retrieval of the yeast general amino acid permease from the vacuolar targeting pathway." Rubio-Texeira M., Kaiser C.A. Mol. Biol. Cell 17:3031-3050(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[27]	"Dual mechanisms specify Doa4-mediated deubiquitination at multivesicular bodies." Richter C., West M., Odorizzi G. EMBO J. 26:2454-2464(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH BRO1, MUTAGENESIS OF CYS-571; TYR-826; PRO-827 AND LEU-829.
[28]	"Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase." Nikko E., Andre B. Eukaryot. Cell 6:1266-1277(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH BRO1, SUBCELLULAR LOCATION.
[29]	"Evidence for a direct role of the Doa4 deubiquitinating enzyme in protein sorting into the MVB pathway." Nikko E., Andre B. Traffic 8:566-581(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-571.
[30]	"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-443, MASS SPECTROMETRY.
[31]	"An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis." Kimura Y., Yashiroda H., Kudo T., Koitabashi S., Murata S., Kakizuka A., Tanaka K. Cell 137:549-559(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION, INTERACTION WITH RFU1.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U02518 Genomic DNA. Translation: AAC48915.1. L08070 Genomic DNA. Translation: AAA35105.1. Z49209 Genomic DNA. Translation: CAA89098.1. Z46796 Genomic DNA. Translation: CAA86791.1. Z74365 Genomic DNA. Translation: CAA98887.1. X84162 Genomic DNA. Translation: CAA58985.1. BK006938 Genomic DNA. Translation: DAA11915.1.
PIR	S39344.
RefSeq	NP_010354.3. NM_001180377.3.
3D structure databases
ProteinModelPortal	P32571.
SMR	P32571. Positions 563-922.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5298N.
IntAct	P32571. 27 interactions.
MINT	MINT-550253.
STRING	4932.YDR069C.
Protein family/group databases
MEROPS	C19.005.
Proteomic databases
PaxDb	P32571.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR069C; YDR069C; YDR069C.
GeneID	851641.
KEGG	sce:YDR069C.
Organism-specific databases
CYGD	YDR069c.
SGD	S000002476. DOA4.
Phylogenomic databases
eggNOG	COG5533.
GeneTree	ENSGT00730000110249.
HOGENOM	HOG000248489.
KO	K11839.
OMA	EDLNQCG.
OrthoDB	EOG7R2BSX.
Enzyme and pathway databases
BioCyc	YEAST:G3O-29676-MONOMER.
Gene expression databases
Genevestigator	P32571.
Family and domain databases
Gene3D	3.40.250.10. 1 hit.
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19/C67. IPR001763. Rhodanese-like_dom. [Graphical view]
Pfam	PF00581. Rhodanese. 1 hit. PF00443. UCH. 1 hit. [Graphical view]
SMART	SM00450. RHOD. 1 hit. [Graphical view]
SUPFAM	SSF52821. SSF52821. 1 hit.
PROSITE	PS50206. RHODANESE_3. 1 hit. PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	969209.

Entry information

Entry name

UBP4_YEAST

Accession

Primary (citable) accession number: P32571
Secondary accession number(s): D6VS55

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	February 1, 1994
Last modified:	November 13, 2013
This is version 142 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Peptidase families

Classification of peptidase families and list of entries

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents