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P35127

- UBL1_YEAST

UniProt

P35127 - UBL1_YEAST

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Protein

Ubiquitin carboxyl-terminal hydrolase YUH1

Gene
YUH1, YJR099W, J1941
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Deubiquitinating enzyme (DUB) that controls levels of cellular ubiquitin through processing of ubiquitin precursors and ubiquitinated proteins. Thiol protease that recognizes and hydrolyzes a peptide bond at the C-terminal glycine of either ubiquitin or RUB1. Preferentially cleaves ubiquitin from peptides and small adducts.4 Publications

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).1 Publication

pH dependencei

Optimum pH is 8.5. Inactive at a pH below 6.5.1 Publication

Temperature dependencei

Optimum temperature is 27 degrees Celsius.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei84 – 841Transition state stabilizer
Active sitei90 – 901Nucleophile By similarity
Active sitei166 – 1661Proton donor By similarity
Sitei181 – 1811Important for enzyme activity By similarity

GO - Molecular functioni

  1. ubiquitin-specific protease activity Source: SGD

GO - Biological processi

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

Keywords - Molecular functioni

Hydrolase, Protease, Thiol protease

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-31727-MONOMER.
BRENDAi3.4.19.12. 984.

Protein family/group databases

MEROPSiC12.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin carboxyl-terminal hydrolase YUH1 (EC:3.4.19.12)
Short name:
UCH
Alternative name(s):
Ubiquitin thioesterase
Gene namesi
Name:YUH1
Ordered Locus Names:YJR099W
ORF Names:J1941
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome X

Organism-specific databases

CYGDiYJR099w.
SGDiS000003860. YUH1.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 236236Ubiquitin carboxyl-terminal hydrolase YUH1PRO_0000211073Add
BLAST

Proteomic databases

MaxQBiP35127.
PaxDbiP35127.

Expressioni

Gene expression databases

GenevestigatoriP35127.

Interactioni

Protein-protein interaction databases

BioGridi33854. 33 interactions.
DIPiDIP-5052N.
IntActiP35127. 1 interaction.
MINTiMINT-488470.
STRINGi4932.YJR099W.

Structurei

Secondary structure

1
236
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi15 – 2511
Beta strandi31 – 366
Helixi44 – 463
Beta strandi54 – 607
Helixi90 – 10011
Helixi103 – 1053
Helixi111 – 12212
Beta strandi126 – 1294
Helixi132 – 14312
Helixi146 – 1505
Beta strandi152 – 1543
Beta strandi164 – 1729
Beta strandi174 – 1807
Beta strandi189 – 1935
Helixi201 – 2033
Helixi205 – 22117
Beta strandi227 – 2337

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CMXX-ray2.25A/C1-235[»]
ProteinModelPortaliP35127.
SMRiP35127. Positions 6-234.

Miscellaneous databases

EvolutionaryTraceiP35127.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 156Interaction with ubiquitin
Regioni149 – 1579Interaction with ubiquitin
Regioni219 – 22810Interaction with ubiquitin

Sequence similaritiesi

Belongs to the peptidase C12 family.

Phylogenomic databases

eggNOGiNOG327708.
GeneTreeiENSGT00510000046640.
HOGENOMiHOG000182400.
KOiK05609.
OMAiYMENANE.
OrthoDBiEOG7PGF2F.

Family and domain databases

Gene3Di3.40.532.10. 1 hit.
InterProiIPR001578. Peptidase_C12_UCH.
[Graphical view]
PANTHERiPTHR10589. PTHR10589. 1 hit.
PfamiPF01088. Peptidase_C12. 1 hit.
[Graphical view]
PRINTSiPR00707. UBCTHYDRLASE.
PROSITEiPS00140. UCH_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P35127-1 [UniParc]FASTAAdd to Basket

« Hide

MSGENRAVVP IESNPEVFTN FAHKLGLKNE WAYFDIYSLT EPELLAFLPR    50
PVKAIVLLFP INEDRKSSTS QQITSSYDVI WFKQSVKNAC GLYAILHSLS 100
NNQSLLEPGS DLDNFLKSQS DTSSSKNRFD DVTTDQFVLN VIKENVQTFS 150
TGQSEAPEAT ADTNLHYITY VEENGGIFEL DGRNLSGPLY LGKSDPTATD 200
LIEQELVRVR VASYMENANE EDVLNFAMLG LGPNWE 236
Length:236
Mass (Da):26,385
Last modified:February 1, 1994 - v1
Checksum:iD239FEE25798B395
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49599 Genomic DNA. Translation: CAA89629.1.
BK006943 Genomic DNA. Translation: DAA08884.1.
PIRiS51332.
RefSeqiNP_012633.1. NM_001181757.1.

Genome annotation databases

EnsemblFungiiYJR099W; YJR099W; YJR099W.
GeneIDi853562.
KEGGisce:YJR099W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49599 Genomic DNA. Translation: CAA89629.1 .
BK006943 Genomic DNA. Translation: DAA08884.1 .
PIRi S51332.
RefSeqi NP_012633.1. NM_001181757.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CMX X-ray 2.25 A/C 1-235 [» ]
ProteinModelPortali P35127.
SMRi P35127. Positions 6-234.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33854. 33 interactions.
DIPi DIP-5052N.
IntActi P35127. 1 interaction.
MINTi MINT-488470.
STRINGi 4932.YJR099W.

Protein family/group databases

MEROPSi C12.002.

Proteomic databases

MaxQBi P35127.
PaxDbi P35127.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YJR099W ; YJR099W ; YJR099W .
GeneIDi 853562.
KEGGi sce:YJR099W.

Organism-specific databases

CYGDi YJR099w.
SGDi S000003860. YUH1.

Phylogenomic databases

eggNOGi NOG327708.
GeneTreei ENSGT00510000046640.
HOGENOMi HOG000182400.
KOi K05609.
OMAi YMENANE.
OrthoDBi EOG7PGF2F.

Enzyme and pathway databases

BioCyci YEAST:G3O-31727-MONOMER.
BRENDAi 3.4.19.12. 984.

Miscellaneous databases

EvolutionaryTracei P35127.
NextBioi 974317.
PROi P35127.

Gene expression databases

Genevestigatori P35127.

Family and domain databases

Gene3Di 3.40.532.10. 1 hit.
InterProi IPR001578. Peptidase_C12_UCH.
[Graphical view ]
PANTHERi PTHR10589. PTHR10589. 1 hit.
Pfami PF01088. Peptidase_C12. 1 hit.
[Graphical view ]
PRINTSi PR00707. UBCTHYDRLASE.
PROSITEi PS00140. UCH_1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and expression of a yeast ubiquitin-protein cleaving activity in Escherichia coli."
    Miller H.I., Henzel W.J., Ridgway J.B., Kuang W.-J., Chisholm V., Liu C.-C.
    Biotechnology (N.Y.) 7:698-704(1989)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Purification of a ubiquitin protein peptidase from yeast with efficient in vitro assays."
    Liu C.C., Miller H.I., Kohr W.J., Silber J.I.
    J. Biol. Chem. 264:20331-20338(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes."
    Layfield R., Franklin K., Landon M., Walker G., Wang P., Ramage R., Brown A., Love S., Urquhart K., Muir T., Baker R., Mayer R.J.
    Anal. Biochem. 274:40-49(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
  6. "Rub1p processing by Yuh1p is required for wild-type levels of Rub1p conjugation to Cdc53p."
    Linghu B., Callis J., Goebl M.G.
    Eukaryot. Cell 1:491-494(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN RUB1 PROCESSING.
  7. "Characterization of ubiquitin C-terminal hydrolase 1 (YUH1) from Saccharomyces cerevisiae expressed in recombinant Escherichia coli."
    Yu H.A., Kim S.G., Kim E.J., Lee W.J., Kim D.O., Park K., Park Y.C., Seo J.H.
    Protein Expr. Purif. 56:20-26(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
  8. "Mutant ubiquitin (UBB(+1)) associated with neurodegenerative disorders is hydrolyzed by ubiquitin C-terminal hydrolase L3 (UCH-L3)."
    Dennissen F.J., Kholod N., Hermes D.J., Kemmerling N., Steinbusch H.W., Dantuma N.P., van Leeuwen F.W.
    FEBS Lett. 585:2568-2574(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN UBB(+1) HYDROLYSIS.
  9. "Structural basis for the specificity of ubiquitin C-terminal hydrolases."
    Johnston S.C., Riddle S.M., Cohen R.E., Hill C.P.
    EMBO J. 18:3877-3887(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH UBIQUITIN, ACTIVE SITE.

Entry informationi

Entry nameiUBL1_YEAST
AccessioniPrimary (citable) accession number: P35127
Secondary accession number(s): D6VWR8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: May 14, 2014
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Can hydrolyze human UBB(+1), a mutated form of ubiquitin which is not effectively degraded by the proteasome and is associated with neurogenerative disorders. It can do so despite of the fact that the C-terminal 'Gly-76' of ubiquitin has been substituted for a tyrosine in UBB(+1).

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

External Data

Dasty 3

Similar proteinsi