Q5BKP2 (UBP13_MOUSE) 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 thioesterase 13
Ubiquitin-specific-processing protease 13

Gene names

Name:

Usp13

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	858 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data By similarity.
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).
Enzyme regulation	Specifically inhibited by spautin-1 (specific and potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13 and inhibits deubiquitinase activity. Regulated by PIK3C3/VPS34-containing complexes. The weak deubiquitinase activity in vitro suggests the existence of some mechanism that activates the enzyme By similarity.
Subunit structure	Interacts with UFD1. Interacts (via UBA domains) with SIAH2 (when ubiquitinated) By similarity.
Domain	The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin By similarity. The UBA domains mediate binding to ubiquitin By similarity.
Sequence similarities	Belongs to the peptidase C19 family. Contains 2 UBA domains. Contains 1 UBP-type zinc finger.

Ontologies

Keywords
Biological process	Autophagy Ubl conjugation pathway
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	autophagy Inferred from electronic annotation. Source: UniProtKB-KW cell proliferation Inferred from sequence or structural similarity. Source: UniProtKB protein K63-linked deubiquitination Inferred from sequence or structural similarity. Source: UniProtKB protein stabilization Inferred from sequence or structural similarity. Source: UniProtKB regulation of autophagy Inferred from sequence or structural similarity. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from sequence or structural similarity. Source: UniProtKB ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	cysteine-type endopeptidase activity Inferred from sequence or structural similarity. Source: UniProtKB omega peptidase activity Inferred from electronic annotation. Source: InterPro ubiquitin binding Inferred from sequence or structural similarity. Source: UniProtKB ubiquitin thiolesterase activity Inferred from sequence or structural similarity. Source: UniProtKB ubiquitin-specific protease activity Inferred from sequence or structural similarity. Source: UniProtKB zinc ion binding 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 – 858	858	Ubiquitin carboxyl-terminal hydrolase 13		PRO_0000418011
Regions
	Domain	650 – 691	42	UBA 1
	Domain	722 – 762	41	UBA 2
	Zinc finger	207 – 279	73	UBP-type
Sites
	Active site	343	1	Nucleophile By similarity
	Active site	818	1	Proton acceptor By similarity
Amino acid modifications
	Modified residue	112	1	Phosphoserine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5BKP2 [UniParc]. Last modified April 12, 2005. Version 1. Checksum: 04989BACB784192C	FASTA	858	96,723
	10 20 30 40 50 60 MQRRGALFSV PGGGGKMAAG DLGELLVPHM PTIRVPRSGD RVYKNECAFS YDSPNSEGGL 70 80 90 100 110 120 YVCMNTFLAF GREHVERHFR KTGQSVYMHL KRHMREKVRG ASGGALPKRR NSKIFLDLDM 130 140 150 160 170 180 DDDLNSDDYE YEDEAKLVIF PDHYEIALPN IEELPALVTI ACDAVLSSKS PYRKQDPDTW 190 200 210 220 230 240 ENEVPVSKYA NNLVQLDNGV RIPPSGWKCA RCDLRENLWL NLTDGSVLCG KWFFDSSGGN 250 260 270 280 290 300 GHALEHYRDM GYPLAVKLGT ITPDGADVYS FQEEGPVSDP HLAKHLAHFG IDMLHTQGTE 310 320 330 340 350 360 NGLRDNDIKP RVSEWEVIQE SGTKLKPMYG PGYTGLKNLG NSCYLSSVMQ AIFSIPEFQR 370 380 390 400 410 420 AYVGNLPRIF DYSPLDPTQD FNTQMTKLGH GLLSGQYSKP PVKSELIEQV MKEEHKPQQN 430 440 450 460 470 480 GISPRMFKAF VSKSHPEFSS NRQQDAQEFF LHLVNLVERN RIGSENPSDV FRFLVEERIQ 490 500 510 520 530 540 CCQTRKVRYT ERVDYLMQLP VAMEAATNKD ELITYELMRR EAEANRRPLP ELVRAKIPFS 550 560 570 580 590 600 ACLQAFAEPD NVDDFWSSAL QAKSAGVKTS RFASFPEYLV VQIKKFTFGL DWVPRKFDVS 610 620 630 640 650 660 IDMPDLLDIS HLRARGLQPG EEELPDISPP IVIPDDSKDR LMNQLIDPSD IDESSVMQLA 670 680 690 700 710 720 EMGFPLEACR KAVYFTGNTG AEVAFNWIIV HMEEPDFAEP LAIPGYGGAG ASVFGATGLD 730 740 750 760 770 780 NQPPEEIVAI ITSMGFQRNQ AVQALQATNH NLERALDWIF SHPEFEEDSD FVIEMENNAN 790 800 810 820 830 840 ANIVSEAKPE GPRVKDGSGM YELFAFISHM GTSTMSGHYV CHIKKEGRWV IYNDHKVCAS 850 ERPPKDLGYM YFYRRIPS

References

[1]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[2]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Heart.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AC111140 Genomic DNA. No translation available. CH466530 Genomic DNA. Translation: EDL35015.1. BC090999 mRNA. Translation: AAH90999.1.
IPI	IPI00134255.
RefSeq	NP_001013042.1. NM_001013024.2.
UniGene	Mm.316153.
3D structure databases
ProteinModelPortal	Q5BKP2.
SMR	Q5BKP2. Positions 24-858.
ModBase	Search...
Protein-protein interaction databases
STRING	10090.ENSMUSP00000072155.
Protein family/group databases
MEROPS	C19.012.
PTM databases
PhosphoSite	Q5BKP2.
Proteomic databases
PaxDb	Q5BKP2.
PRIDE	Q5BKP2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000072312; ENSMUSP00000072155; ENSMUSG00000056900.
GeneID	72607.
KEGG	mmu:72607.
UCSC	uc008owr.1. mouse.
Organism-specific databases
CTD	8975.
MGI	MGI:1919857. Usp13.
Phylogenomic databases
eggNOG	COG5207.
GeneTree	ENSGT00390000000874.
HOGENOM	HOG000162311.
HOVERGEN	HBG002833.
InParanoid	Q5BKP2.
KO	K11836.
OMA	PQQNGIS.
OrthoDB	EOG46DM24.
Gene expression databases
ArrayExpress	Q5BKP2.
Bgee	Q5BKP2.
Genevestigator	Q5BKP2.
Family and domain databases
Gene3D	3.30.40.10. 1 hit.
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. IPR009060. UBA-like. IPR000449. UBA/transl_elong_EF1B_N. IPR015940. UBA/transl_elong_EF1B_N_euk. IPR016652. Ubiquitinyl_hydrolase. IPR013083. Znf_RING/FYVE/PHD. IPR001607. Znf_UBP. [Graphical view]
Pfam	PF00627. UBA. 2 hits. PF00443. UCH. 1 hit. PF02148. zf-UBP. 1 hit. [Graphical view]
PIRSF	PIRSF016308. UBP. 1 hit.
SMART	SM00165. UBA. 2 hits. SM00290. ZnF_UBP. 1 hit. [Graphical view]
SUPFAM	SSF46934. UBA_like. 1 hit.
PROSITE	PS50030. UBA. 2 hits. PS00972. UCH_2_1. 1 hit. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. PS50271. ZF_UBP. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	336585.
SOURCE	Search...

Entry information

Entry name

UBP13_MOUSE

Accession

Primary (citable) accession number: Q5BKP2
Secondary accession number(s): D3YYG7

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2012
Last sequence update:	April 12, 2005
Last modified:	May 1, 2013
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program