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P35127 (UBL1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin carboxyl-terminal hydrolase YUH1

Short name=UCH
EC=3.4.19.12
Alternative name(s):
Ubiquitin thioesterase
Gene names
Name:YUH1
Ordered Locus Names:YJR099W
ORF Names:J1941
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length236 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.6 Ref.7 Ref.8

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). Ref.5

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).

Sequence similarities

Belongs to the peptidase C12 family.

Biophysicochemical properties

pH dependence:

Optimum pH is 8.5. Inactive at a pH below 6.5. Ref.7

Temperature dependence:

Optimum temperature is 27 degrees Celsius.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 236236Ubiquitin carboxyl-terminal hydrolase YUH1
PRO_0000211073

Regions

Region10 – 156Interaction with ubiquitin
Region149 – 1579Interaction with ubiquitin
Region219 – 22810Interaction with ubiquitin

Sites

Active site901Nucleophile By similarity
Active site1661Proton donor By similarity
Site841Transition state stabilizer
Site1811Important for enzyme activity By similarity

Secondary structure

................................... 236
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P35127 [UniParc].

Last modified February 1, 1994. Version 1.
Checksum: D239FEE25798B395

FASTA23626,385
        10         20         30         40         50         60 
MSGENRAVVP IESNPEVFTN FAHKLGLKNE WAYFDIYSLT EPELLAFLPR PVKAIVLLFP 

        70         80         90        100        110        120 
INEDRKSSTS QQITSSYDVI WFKQSVKNAC GLYAILHSLS NNQSLLEPGS DLDNFLKSQS 

       130        140        150        160        170        180 
DTSSSKNRFD DVTTDQFVLN VIKENVQTFS TGQSEAPEAT ADTNLHYITY VEENGGIFEL 

       190        200        210        220        230 
DGRNLSGPLY LGKSDPTATD LIEQELVRVR VASYMENANE EDVLNFAMLG LGPNWE 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z49599 Genomic DNA. Translation: CAA89629.1.
BK006943 Genomic DNA. Translation: DAA08884.1.
PIRS51332.
RefSeqNP_012633.1. NM_001181757.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CMXX-ray2.25A/C1-235[»]
ProteinModelPortalP35127.
SMRP35127. Positions 6-234.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33854. 33 interactions.
DIPDIP-5052N.
IntActP35127. 1 interaction.
MINTMINT-488470.
STRING4932.YJR099W.

Protein family/group databases

MEROPSC12.002.

Proteomic databases

MaxQBP35127.
PaxDbP35127.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYJR099W; YJR099W; YJR099W.
GeneID853562.
KEGGsce:YJR099W.

Organism-specific databases

CYGDYJR099w.
SGDS000003860. YUH1.

Phylogenomic databases

eggNOGNOG327708.
GeneTreeENSGT00510000046640.
HOGENOMHOG000182400.
KOK05609.
OMAYMENANE.
OrthoDBEOG7PGF2F.

Enzyme and pathway databases

BioCycYEAST:G3O-31727-MONOMER.
BRENDA3.4.19.12. 984.

Gene expression databases

GenevestigatorP35127.

Family and domain databases

Gene3D3.40.532.10. 1 hit.
InterProIPR001578. Peptidase_C12_UCH.
[Graphical view]
PANTHERPTHR10589. PTHR10589. 1 hit.
PfamPF01088. Peptidase_C12. 1 hit.
[Graphical view]
PRINTSPR00707. UBCTHYDRLASE.
PROSITEPS00140. UCH_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP35127.
NextBio974317.
PROP35127.

Entry information

Entry nameUBL1_YEAST
AccessionPrimary (citable) accession number: P35127
Secondary accession number(s): D6VWR8
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome X

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references