F6V6I0 (UBP13_XENTR) 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

Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) [Reference proteome]

Taxonomic identifier

8364 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Silurana

Protein attributes

Sequence length	846 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 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 – 846	846	Ubiquitin carboxyl-terminal hydrolase 13		PRO_0000418014
Regions
	Domain	633 – 676	44	UBA 1
	Domain	708 – 748	41	UBA 2
	Zinc finger	190 – 262	73	UBP-type
Sites
	Active site	806	1	Proton acceptor By similarity

Sequences

	Sequence		Length	Mass (Da)
	F6V6I0 [UniParc]. Last modified June 13, 2012. Version 2. Checksum: 139B256C047BE39A	FASTA	846	95,089
	10 20 30 40 50 60 MAEDLGELLV PYMPTIRVPK SGDRVYKTEC AFSYDSPESD GGLYVCMSTF LGFGREHVER 70 80 90 100 110 120 HYRKTGQSVY MHLKRHIRLK ATGASGGAFP KRINGRLFLD LENNTEMNTE DYEYEDEAKL 130 140 150 160 170 180 VIFPDHFEIA LPNIEELPAL VTIACDAVLN SKSPYRKLDQ ESWEEELQVS KFANNLVQID 190 200 210 220 230 240 NGVKIPPSGW KCSKCDLQEN LWLNLTDGSI MCGRWFCSGS GGNGHALEHH KQMGYPLAVR 250 260 270 280 290 300 LGSITPDGAD VYSFDEEEAV IDPHLAKHLA HFGIDMLQMQ GSENGVLDNE VKPRVNEWEV 310 320 330 340 350 360 IQETGLKLKP MFGSGYTGIK NLGNSSYLTT VMQVIFSIPE FQRAYVGNLT RIFDYAPLDP 370 380 390 400 410 420 TQDFSTQMAK LGHGLLSGQF SKPPMKSELI EQVMKEEHKP QPKGINTRMF KALMSKGHTE 430 440 450 460 470 480 FSSNRQQDAE EFFLHFINLV ERNSIGAENP SDVFRFLVEE RTQCCQSRKV RYTERVDYIM 490 500 510 520 530 540 QLPVPMETAT NKEELIAYDL KRREAESAKR PPPELVRAKI PFSACLQAFT EPENVPDFWS 550 560 570 580 590 600 SALQAKSAGV KTSRFASFPE YLVVQIKKFT FGLDWVPKKL DVSIDMPDLL DINHLRATGL 610 620 630 640 650 660 KSGEEELPDI APPIIIPDDP NGRMAESLLS GSGSNVNSSF KGAQPLNLPF GKKEAKLLRY 670 680 690 700 710 720 MERMVEKFGF KFSVRLSVEI DFAEPLIIPG CGTVTSTSSH GQNALLNQPP EEIVALICSM 730 740 750 760 770 780 GFPRNHALQA LRATNNNLER ALDWMFSHPE SEEGADNVSG CVDTENNPNG IITDSEQEGP 790 800 810 820 830 840 RIKDGNGRYE LFGIISHAGT STMSGHYVCH IKKEGRWVIY NDHKVSASER PPKELGYIYF YHRISC

References

[1]

"The genome of the Western clawed frog Xenopus tropicalis." Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J., Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L., Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R., Gerhard D.S. , Goodstein D., Graves T., Grigoriev I.V., Grimwood J., Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H., Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K., Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A., Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R., Grammer T., Khokha M.K., Richardson P.M., Rokhsar D.S. Science 328:633-636(2010) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAMC01001929 Genomic DNA. No translation available. AAMC01001930 Genomic DNA. No translation available. AAMC01001931 Genomic DNA. No translation available. AAMC01001932 Genomic DNA. No translation available. AAMC01001933 Genomic DNA. No translation available. AAMC01001934 Genomic DNA. No translation available.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Family and domain databases
Gene3D	3.30.40.10. 1 hit.
InterPro	IPR018200. Pept_C19ubi-hydrolase_C_CS. IPR001394. Peptidase_C19. 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. 1 hit. PF00443. UCH. 1 hit. PF02148. zf-UBP. 1 hit. [Graphical view]
PIRSF	PIRSF016308. UBP. 1 hit.
SMART	SM00165. UBA. 1 hit. SM00290. ZnF_UBP. 1 hit. [Graphical view]
PROSITE	PS50030. UBA. 1 hit. 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...

Entry information

Entry name

UBP13_XENTR

Accession

Primary (citable) accession number: F6V6I0

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2012
Last sequence update:	June 13, 2012
Last modified:	April 3, 2013
This is version 15 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program