F1QFS9 (UBP13_DANRE) 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
ORF Names:	wu:fc61g08

Organism

Danio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]

Taxonomic identifier

7955 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Actinopterygii › Actinopteri › Neopterygii › Teleostei › Elopocephala › Clupeocephala › Otocephala › Ostariophysi › Otophysi › Cypriniphysi › Cypriniformes › Cyprinoidea › Cyprinidae › Danio

Protein attributes

Sequence length	860 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Deubiquitinase that mediates deubiquitination of target proteins and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD) 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 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
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 dorsal/ventral pattern formation Inferred from mutant phenotype PubMed 20040115. Source: ZFIN 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 – 860	860	Ubiquitin carboxyl-terminal hydrolase 13		PRO_0000418013
Regions
	Domain	635 – 676	42	UBA 1
	Domain	710 – 750	41	UBA 2
	Zinc finger	190 – 262	73	UBP-type
Sites
	Active site	327	1	Nucleophile By similarity
	Active site	819	1	Proton acceptor By similarity
Experimental info
	Sequence conflict	731	1	Q → R in AAI41801. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	F1QFS9 [UniParc]. Last modified May 3, 2011. Version 1. Checksum: 456C6827F7D0DCC1	FASTA	860	97,452
	10 20 30 40 50 60 MATDLGELLV PYMPTIRVPR TGDRVFKSEC AFSYDSPESE GGLYVCMNSF LGFGREHVER 70 80 90 100 110 120 HYRKTGQSVY MHLKRHVKEK ATGAAGGAIP RRRNGKVFLD LELNRDFNGD DYEYEDEAKL 130 140 150 160 170 180 VIFPDHYEIP LPNIEELPAL VTIACDAVLN APSPYKKQES DSWEEEIQVS RHARSLRQLD 190 200 210 220 230 240 NGVRIPPSGW KCAKCEMREN LWLNLTDGSV LCGKWFFDGS GGNGHALEHY RESNFPLAVK 250 260 270 280 290 300 LNTITPDGAD IYSFDEEEAV LDPHISEHLL HFGIDMLQMQ RTENGHHTDN HVQPRISDWE 310 320 330 340 350 360 VIQEAGLKLK PVYGSGYTGI KNLGNSCYLS TTMQVLFSIP EFQRAYAGNL QRIFDYSPLD 370 380 390 400 410 420 PTQDFNTQMA KLGHGLLSGQ YSKPPMKSEL IEQVMKEEHK QQQQRGISPK MFKALVSKGH 430 440 450 460 470 480 PEFSSNRQQD AHEFLLHLIN LVERNNSGSE NPSDVFRFIV EERTQCCQSQ KVRYTQRVDY 490 500 510 520 530 540 LMQLPVPLEA ASNREELIAY EGKRKEAEEN MRPLPEVVRA RVPFTACLQA FTEPENVPDF 550 560 570 580 590 600 WSSALQAKSA GVKTSRFATF PEYMIVQLKK FTFGVDWVPK KLDMSVDVPD FLDLNRLRAT 610 620 630 640 650 660 GLQAGEEELP DLTPPIVIPE DTRDSSTNNS LESPEIDESS VMQLAEMGFP LEACRKAVYY 670 680 690 700 710 720 TGNMGAEMAF NWIIAHMEEP DFAEPLAVPT YMESDLPSPS LPTTSALDNQ PPEESISILT 730 740 750 760 770 780 SMGFPRHHTI QALKASNNNL ERALDWIFTH PDCEDESEAM SDTADTEPND NSFSNANAHT 790 800 810 820 830 840 DSSLSPDQDL SSPRVRDGPG RYELFAFISH MGTSTMSGHY VCHIKKEGRW LIYNDHKVCL 850 860 SERPPKDLGY MYFYRRLSSC

References

[1]	The Danio rerio sequencing project at the Sanger Institute Submitted (JUL-2010) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Tuebingen.
[2]	NIH - Zebrafish Gene Collection (ZGC) project Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Embryo.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL928701 Genomic DNA. No translation available. CU459215 Genomic DNA. No translation available. BC141800 mRNA. Translation: AAI41801.1.
IPI	IPI00636029.
RefSeq	NP_001091856.1. NM_001098386.1.
UniGene	Dr.115281.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	7955.ENSDARP00000095070.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSDART00000065293; ENSDARP00000065292; ENSDARG00000079198.
GeneID	558011.
KEGG	dre:558011.
Organism-specific databases
CTD	8975.
ZFIN	ZDB-GENE-040426-2584. usp5.
Phylogenomic databases
GeneTree	ENSGT00390000000874.
KO	K11836.
OMA	PQQNGIS.
Gene expression databases
Bgee	F1QFS9.
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. False negative. PS00973. UCH_2_2. 1 hit. PS50235. UCH_2_3. 1 hit. PS50271. ZF_UBP. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	20882266.

Entry information

Entry name

UBP13_DANRE

Accession

Primary (citable) accession number: F1QFS9
Secondary accession number(s): A5D8T1

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2012
Last sequence update:	May 3, 2011
Last modified:	April 3, 2013
This is version 19 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program