P35127 (UBL1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	236 AA.
Sequence status	Complete.
Protein existence	Evidence 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.9
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.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred by curator PubMed 1429680. Source: SGD
Molecular_function	cysteine-type peptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 236

236

Ubiquitin carboxyl-terminal hydrolase YUH1

PRO_0000211073

Regions

Region

10 – 15

6

Interaction with ubiquitin

Region

149 – 157

9

Interaction with ubiquitin

Region

219 – 228

10

Interaction with ubiquitin

Sites

Active site

90

1

Nucleophile By similarity

Active site

166

1

Proton donor By similarity

Site

84

1

Transition state stabilizer

Site

181

1

Important for enzyme activity By similarity

Amino acid modifications

Modified residue

186

1

Phosphoserine Ref.8

Secondary structure

1

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236

Helix Strand Turn

Details...

Helix

15 – 25

11

Beta strand

31 – 36

6

Helix

44 – 46

3

Beta strand

54 – 60

7

Helix

90 – 100

11

Helix

103 – 105

3

Helix

111 – 122

12

Beta strand

126 – 129

4

Helix

132 – 143

12

Helix

146 – 150

5

Beta strand

152 – 154

3

Beta strand

164 – 172

9

Beta strand

174 – 180

7

Beta strand

189 – 193

5

Helix

201 – 203

3

Helix

205 – 221

17

Beta strand

227 – 233

7

Sequences

	Sequence		Length	Mass (Da)
	P35127 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: D239FEE25798B395	FASTA	236	26,385
	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

References

	« Hide 'large scale' referencesShow '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. , 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 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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]	"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-186, MASS SPECTROMETRY.
[9]	"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.
[10]	"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.

PIR

S51332.

RefSeq

NP_012633.1. NM_001181757.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CMX	X-ray	2.25	A/C	1-235	[»]

ProteinModelPortal

P35127.

SMR

P35127. Positions 6-234.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5052N.

IntAct

P35127. 1 interaction.

MINT

MINT-488470.

STRING

4932.YJR099W.

Protein family/group databases

MEROPS

C12.002.

Proteomic databases

PaxDb

P35127.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YJR099W; YJR099W; YJR099W.

GeneID

853562.

KEGG

sce:YJR099W.

Organism-specific databases

CYGD

YJR099w.

SGD

S000003860. YUH1.

Phylogenomic databases

eggNOG

NOG327708.

GeneTree

ENSGT00510000046640.

HOGENOM

HOG000182400.

KO

K05609.

OMA

VIEHYIC.

OrthoDB

EOG4FR41W.

Enzyme and pathway databases

BRENDA

3.4.19.12. 984.

Gene expression databases

Genevestigator

P35127.

GermOnline

YJR099W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.40.532.10. 1 hit.

InterPro

IPR001578. Peptidase_C12.
[Graphical view]

PANTHER

PTHR10589. PTHR10589. 1 hit.

Pfam

PF01088. Peptidase_C12. 1 hit.
[Graphical view]

PRINTS

PR00707. UBCTHYDRLASE.

PROSITE

PS00140. UCH_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P35127.

NextBio

974317.

Entry information

Entry name

UBL1_YEAST

Accession

Primary (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:	April 3, 2013
This is version 116 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program