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B3LGK1

- UBP4_YEAS1

UniProt

B3LGK1 - UBP4_YEAS1

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Protein

Ubiquitin carboxyl-terminal hydrolase 4

Gene
DOA4, DOS1, MUT4, NPI2, SSV7, UBP4, SCRG_00446
Organism
Saccharomyces cerevisiae (strain RM11-1a) (Baker's yeast)
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

Functioni

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 By similarity.

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).

Enzyme regulationi

RFU1 is an inhibitor of deubiquitination activity By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei571 – 5711Nucleophile By similarity
Active sitei880 – 8801Proton acceptor By similarity

GO - Molecular functioni

  1. cysteine-type peptidase activity Source: UniProtKB-KW
  2. ubiquitinyl hydrolase activity Source: InterPro

GO - Biological processi

  1. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Names & Taxonomyi

Protein namesi
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 namesi
Name:DOA4
Synonyms:DOS1, MUT4, NPI2, SSV7, UBP4
ORF Names:SCRG_00446
OrganismiSaccharomyces cerevisiae (strain RM11-1a) (Baker's yeast)
Taxonomic identifieri285006 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000008335: Unassembled WGS sequence

Subcellular locationi

Cytoplasm By similarity. Late endosome membrane; Peripheral membrane protein By similarity
Note: Recruited to the late endosome by BRO1 By similarity.

GO - Cellular componenti

  1. late endosome membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 926926Ubiquitin carboxyl-terminal hydrolase 4PRO_0000376822Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei443 – 4431Phosphoserine By similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Interacts with BRO1, RFU1 and VPS32. Associates with the 26S proteasome By similarity.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini205 – 328124RhodaneseAdd
BLAST
Domaini562 – 923362USPAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi128 – 1347Poly-Asn
Compositional biasi386 – 3927Poly-Gln

Domaini

Residues 1-208 are essential for the localization to the late endosome and constitute a late endosome localization (LEL) domain By similarity.

Sequence similaritiesi

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

Phylogenomic databases

OrthoDBiEOG7R2BSX.

Family and domain databases

Gene3Di3.40.250.10. 1 hit.
InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR001763. Rhodanese-like_dom.
IPR028889. UCH/PAN2.
[Graphical view]
PfamiPF00581. Rhodanese. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view]
SMARTiSM00450. RHOD. 1 hit.
[Graphical view]
SUPFAMiSSF52821. SSF52821. 1 hit.
PROSITEiPS50206. RHODANESE_3. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B3LGK1-1 [UniParc]FASTAAdd to Basket

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MEQNIISTIR DECIRHRSKY LTIAQLTAIA EAKINEFIIT GKAKDQDLSS    50
LLDKCIDILS IYKKNSKDIK NIISCKNKGA MISSNSVMII QLNYVYYKVI 100
HIIVTTNIPH LSEFAKIKLH KSTSDEGNGN NNNNEFQLMN IYNTLLETLL 150
KDENIAKIKS FIKSSIKQTK LNHEQEECNL MRTGSYITSN QLNSLISSSA 200
NSASSQMEIL LIDIRSRLEF NKSHIDTKNI ICLEPISFKM SYSDHDLEKK 250
SLITSPNSEI KMFQSRNLFK FIILYTDANE YNVKQQSVLL DILVNHSFEK 300
PISDDFTKIF ILESGFPGWL KSNYGRQVSS SFPSNNNIKD DSVYINGNTS 350
GLSLQHLPKM SPSIRHSMDD SMKEMLVAPT PLNHLQQQQQ QQSDNDHVLK 400
RSSSFKKLFS NYTSPNPKNS NSNLYSISSL SISSSPSPLP LHSPDPVKGN 450
SLPINYPETP HLWKNSETDF MTNQREQLNH NSFAHVAPIN TKAITSPSRT 500
ATPKLQRFPQ TISMNLNMNS NGHSSATSTI QPSCLSLSNN DSLDHTDVTP 550
TSSHNYDLDF AVGLENLGNS CYMNCIIQCI LGTHELTQIF LDDSYAKHIN 600
INSKLGSKGI LAKYFARLVH MMYKEQVDGS KKIPISPIKF KLACGSVNSL 650
FKTASQQDCQ EFCQFLLDGL HEDLNQCGSN PPLKELSQEA EARREKLSLR 700
IASSIEWERF LTTDFSVIVD LFQGQYASRL KCKVCSHTST TYQPFTVLSI 750
PIPKKNSRNN ITIEDCFREF TKCENLEVDE QWLCPHCEKR QPSTKQLTIT 800
RLPRNLIVHL KRFDNLLNKN NDFVIYPFLL DLTPFWANDF DGVFPPGVND 850
DELPIRGQIP PFKYELYGVA CHFGTLYGGH YTAYVKKGLK KGWLYFDDTK 900
YKPVKNKADA INSNAYVLFY HRVYGV 926
Length:926
Mass (Da):105,188
Last modified:September 2, 2008 - v1
Checksum:iBE75CFBAE9C1A9F6
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CH408043 Genomic DNA. Translation: EDV08230.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CH408043 Genomic DNA. Translation: EDV08230.1 .

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Phylogenomic databases

OrthoDBi EOG7R2BSX.

Family and domain databases

Gene3Di 3.40.250.10. 1 hit.
InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR001763. Rhodanese-like_dom.
IPR028889. UCH/PAN2.
[Graphical view ]
Pfami PF00581. Rhodanese. 1 hit.
PF00443. UCH. 1 hit.
[Graphical view ]
SMARTi SM00450. RHOD. 1 hit.
[Graphical view ]
SUPFAMi SSF52821. SSF52821. 1 hit.
PROSITEi PS50206. RHODANESE_3. 1 hit.
PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RM11-1a.

Entry informationi

Entry nameiUBP4_YEAS1
AccessioniPrimary (citable) accession number: B3LGK1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2009
Last sequence update: September 2, 2008
Last modified: September 3, 2014
This is version 29 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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