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P38187

- UBP13_YEAST

UniProt

P38187 - UBP13_YEAST

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Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

UBP13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

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 sitei149 – 1491NucleophilePROSITE-ProRule annotation
Active sitei619 – 6191Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: SGD

GO - Biological processi

  1. free ubiquitin chain depolymerization Source: SGD
  2. ubiquitin-dependent protein catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-28963-MONOMER.

Protein family/group databases

MEROPSiC19.100.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
Alternative name(s):
Deubiquitinating enzyme 13
Ubiquitin thioesterase 13
Ubiquitin-specific-processing protease 13
Gene namesi
Name:UBP13
Ordered Locus Names:YBL067C
ORF Names:YBL0621
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome II

Organism-specific databases

CYGDiYBL067c.
SGDiS000000163. UBP13.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 747747Ubiquitin carboxyl-terminal hydrolase 13PRO_0000080598Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei198 – 1981Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38187.
PaxDbiP38187.

Expressioni

Gene expression databases

GenevestigatoriP38187.

Interactioni

Protein-protein interaction databases

BioGridi32633. 103 interactions.
DIPiDIP-795N.
IntActiP38187. 2 interactions.
MINTiMINT-2783268.
STRINGi4932.YBL067C.

Structurei

3D structure databases

ProteinModelPortaliP38187.
SMRiP38187. Positions 431-665.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini140 – 668529USPAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG5077.
GeneTreeiENSGT00650000093027.
HOGENOMiHOG000141813.
InParanoidiP38187.
KOiK11872.
OMAiHESTARP.
OrthoDBiEOG7TF7JV.

Family and domain databases

InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view]
PfamiPF00443. 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.

P38187-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIRRWLTISK SGKKKKAVND TITEEVEKVD FKPVNHDIND ELCYSESSDN
60 70 80 90 100
PSSSLFVSNL DTKETFLNED NNLQISSGLD YSSETCNQGS NYSQDGIFYI
110 120 130 140 150
SNAKAINAYG GIITQGPEAP ILAMKVSDSM PYGDGSNKVF GYENFGNTCY
160 170 180 190 200
CNSVLQCLYN LSSLRENILQ FPKKSRESDQ PRKKEMRGKK PRIFTEASFE
210 220 230 240 250
KSIAGTNGHL PNPKPQSVDD GKPTPVNSVN SNTAGPSEKK SKFFKSFSAK
260 270 280 290 300
HVQDNNKKEG SPAILTTGKP SSRPQDAPPL IVETPNEPGA PSRLSFENVT
310 320 330 340 350
DRPPDVPRKI IVGRVLNYEN PSRGSSNSNN LDLKGESNSS LSTPLDKKDT
360 370 380 390 400
RRSSSSSQIS PEHRKKSALI RGPVLNIDHS LNGSDKATLY SSLRDIFECI
410 420 430 440 450
TENTYLTGVV SPSSFVDVLK RENVLFNTTM HQDAHEFFNF LLNELSEYIE
460 470 480 490 500
RENKKIAASD INSDSEPSKS KNFISDLFQG TLTNQIKCLT CDNITSRDEP
510 520 530 540 550
FLDFPIEVQG DEETDIQEIL KSYHQREMLN GSNKFYCDEC CGLQEAERLV
560 570 580 590 600
GLKQLPDTLT LHLKRFKYSE KQNCNIKLFN NIHYPLTLNV CSSINSKVCQ
610 620 630 640 650
KYELAGIVVH MGGGPQHGHY VSLCKHEKFG WLLFDDETVE AVKEETVLEF
660 670 680 690 700
TGESPNMATA YVLFYKAMYS NAVEKNDREN MAKEQDDNID NLIKYDDWLR
710 720 730 740
TCNSGQKKKE ELPIADDLDT AIDDSFVSNT PIKSSKKKSR MFSFRKS
Length:747
Mass (Da):83,856
Last modified:July 27, 2011 - v3
Checksum:i817DE2F89ED8EEA4
GO

Sequence cautioni

The sequence CAA84887.1 differs from that shown. Reason: Frameshift at position 663. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti180 – 1801Q → H in CAA84887. (PubMed:7813418)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35828 Genomic DNA. Translation: CAA84887.1. Frameshift.
BK006936 Genomic DNA. Translation: DAA07054.2.
PIRiS45803.
RefSeqiNP_009486.3. NM_001178307.2.

Genome annotation databases

EnsemblFungiiYBL067C; YBL067C; YBL067C.
GeneIDi852212.
KEGGisce:YBL067C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35828 Genomic DNA. Translation: CAA84887.1 . Frameshift.
BK006936 Genomic DNA. Translation: DAA07054.2 .
PIRi S45803.
RefSeqi NP_009486.3. NM_001178307.2.

3D structure databases

ProteinModelPortali P38187.
SMRi P38187. Positions 431-665.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32633. 103 interactions.
DIPi DIP-795N.
IntActi P38187. 2 interactions.
MINTi MINT-2783268.
STRINGi 4932.YBL067C.

Protein family/group databases

MEROPSi C19.100.

Proteomic databases

MaxQBi P38187.
PaxDbi P38187.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YBL067C ; YBL067C ; YBL067C .
GeneIDi 852212.
KEGGi sce:YBL067C.

Organism-specific databases

CYGDi YBL067c.
SGDi S000000163. UBP13.

Phylogenomic databases

eggNOGi COG5077.
GeneTreei ENSGT00650000093027.
HOGENOMi HOG000141813.
InParanoidi P38187.
KOi K11872.
OMAi HESTARP.
OrthoDBi EOG7TF7JV.

Enzyme and pathway databases

BioCyci YEAST:G3O-28963-MONOMER.

Miscellaneous databases

NextBioi 970718.

Gene expression databases

Genevestigatori P38187.

Family and domain databases

InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
IPR001394. Peptidase_C19_UCH.
IPR028889. UCH/PAN2.
[Graphical view ]
Pfami PF00443. UCH. 1 hit.
[Graphical view ]
PROSITEi PS00972. USP_1. 1 hit.
PS00973. USP_2. 1 hit.
PS50235. USP_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete DNA sequence of yeast chromosome II."
    Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
    , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
    EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 180.
    Strain: ATCC 204508 / S288c.
  3. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
    Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
    Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF FRAMESHIFT.
  4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  5. "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-198, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  6. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiUBP13_YEAST
AccessioniPrimary (citable) accession number: P38187
Secondary accession number(s): D6VPT4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: July 27, 2011
Last modified: October 29, 2014
This is version 117 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 125 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 II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3