P38187 (UBP13_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin carboxyl-terminal hydrolase 13
EC=3.4.19.12

Alternative name(s):
Deubiquitinating enzyme 13
Ubiquitin thiolesterase 13
Ubiquitin-specific-processing protease 13

Gene names

Name:	UBP13
Ordered Locus Names:	YBL067C
ORF Names:	YBL0621

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	747 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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).
Miscellaneous	Present with 125 molecules/cell in log phase SD medium. Ref.4
Sequence similarities	Belongs to the peptidase C19 family.
Sequence caution	The sequence CAA84887.1 differs from that shown. Reason: Frameshift at position 663.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	ubiquitin thiolesterase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Traceable author statement. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 747	747	Ubiquitin carboxyl-terminal hydrolase 13		PRO_0000080598
Sites
	Active site	149	1	Nucleophile By similarity
	Active site	619	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	198	1	Phosphoserine Ref.5 Ref.7
	Modified residue	340	1	Phosphoserine Ref.7
	Modified residue	354	1	Phosphoserine Ref.6
	Modified residue	355	1	Phosphoserine Ref.6
	Modified residue	356	1	Phosphoserine Ref.7
Experimental info
	Sequence conflict	180	1	Q → H in CAA84887. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P38187 [UniParc]. Last modified July 27, 2011. Version 3. Checksum: 817DE2F89ED8EEA4	FASTA	747	83,856
	10 20 30 40 50 60 MIRRWLTISK SGKKKKAVND TITEEVEKVD FKPVNHDIND ELCYSESSDN PSSSLFVSNL 70 80 90 100 110 120 DTKETFLNED NNLQISSGLD YSSETCNQGS NYSQDGIFYI SNAKAINAYG GIITQGPEAP 130 140 150 160 170 180 ILAMKVSDSM PYGDGSNKVF GYENFGNTCY CNSVLQCLYN LSSLRENILQ FPKKSRESDQ 190 200 210 220 230 240 PRKKEMRGKK PRIFTEASFE KSIAGTNGHL PNPKPQSVDD GKPTPVNSVN SNTAGPSEKK 250 260 270 280 290 300 SKFFKSFSAK HVQDNNKKEG SPAILTTGKP SSRPQDAPPL IVETPNEPGA PSRLSFENVT 310 320 330 340 350 360 DRPPDVPRKI IVGRVLNYEN PSRGSSNSNN LDLKGESNSS LSTPLDKKDT RRSSSSSQIS 370 380 390 400 410 420 PEHRKKSALI RGPVLNIDHS LNGSDKATLY SSLRDIFECI TENTYLTGVV SPSSFVDVLK 430 440 450 460 470 480 RENVLFNTTM HQDAHEFFNF LLNELSEYIE RENKKIAASD INSDSEPSKS KNFISDLFQG 490 500 510 520 530 540 TLTNQIKCLT CDNITSRDEP FLDFPIEVQG DEETDIQEIL KSYHQREMLN GSNKFYCDEC 550 560 570 580 590 600 CGLQEAERLV GLKQLPDTLT LHLKRFKYSE KQNCNIKLFN NIHYPLTLNV CSSINSKVCQ 610 620 630 640 650 660 KYELAGIVVH MGGGPQHGHY VSLCKHEKFG WLLFDDETVE AVKEETVLEF TGESPNMATA 670 680 690 700 710 720 YVLFYKAMYS NAVEKNDREN MAKEQDDNID NLIKYDDWLR TCNSGQKKKE ELPIADDLDT 730 740 AIDDSFVSNT PIKSSKKKSR MFSFRKS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 7813418] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases 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: 12748633] [Abstract] Cited for: IDENTIFICATION OF FRAMESHIFT.
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] 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: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, MASS SPECTROMETRY.
[6]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354 AND SER-355, MASS SPECTROMETRY.
[7]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198; SER-340 AND SER-356, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z35828 Genomic DNA. Translation: CAA84887.1. Frameshift. BK006936 Genomic DNA. Translation: DAA07054.2.
PIR	S45803.
RefSeq	NP_009486.3. NM_001178307.2.
3D structure databases
ProteinModelPortal	P38187.
SMR	P38187. Positions 137-170, 411-669.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-795N.
IntAct	P38187. 1 interaction.
MINT	MINT-2783268.
STRING	P38187.
Protein family/group databases
MEROPS	C19.A17.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	852212.
KEGG	sce:YBL067C.
NMPDR	fig|4932.3.peg.175.
Organism-specific databases
CYGD	YBL067c.
SGD	S000000163. UBP13.
Phylogenomic databases
eggNOG	fuNOG06102.
GeneTree	EFGT00050000000212.
HOGENOM	HBG204242.
OMA	IFGMENF.
OrthoDB	EOG43XZCS.
Gene expression databases
ArrayExpress	P38187.
Genevestigator	P38187.
GermOnline	YBL067C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. [Graphical view]
KO	K11872.
Pfam	PF00443. UCH. 1 hit. [Graphical view]
PROSITE	PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	970718.

Entry information

Entry name

UBP13_YEAST

Accession

Primary (citable) accession number: P38187
Secondary accession number(s): D6VPT4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	July 27, 2011
Last modified:	December 14, 2011
This is version 95 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program