E1BY77 (UBP13_CHICK) 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

Gallus gallus (Chicken) [Reference proteome]

Taxonomic identifier

9031 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Sauropsida › Sauria › Archosauria › Dinosauria › Saurischia › Theropoda › Coelurosauria › Aves › Neognathae › Galliformes › Phasianidae › Phasianinae › Gallus

Protein attributes

Sequence length	862 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 – 862	862	Ubiquitin carboxyl-terminal hydrolase 13		PRO_0000418012
Regions
	Domain	647 – 688	42	UBA 1
	Domain	722 – 762	41	UBA 2
	Zinc finger	204 – 276	73	UBP-type
Sites
	Active site	340	1	Nucleophile By similarity
	Active site	822	1	Proton acceptor By similarity

Sequences

	Sequence		Length	Mass (Da)
	E1BY77 [UniParc]. Last modified November 2, 2010. Version 1. Checksum: 9207A3B6846A1018	FASTA	862	96,649
	10 20 30 40 50 60 MQRAALFGGG DAQMAAGDLG ELLVPYMPTI RVPKSGDRVY KTECAFSYDS PDSEGGLYVC 70 80 90 100 110 120 MNTFLGFGRE HIERHYRKTG QCVYLHLKRH VIEKVPGASG GALPKRRNAK LFLDLEANGD 130 140 150 160 170 180 LSSDDFEYED EAKLVIFPDH YEISLPNIEE LPALVTIASD ALLSAKSPYR KQDPDSWEEE 190 200 210 220 230 240 LQASKHAKSL VQLDNGVRIP PSGWKCSKCD LRENLWLNLT DGSVLCGKWF FDGSGGNGHA 250 260 270 280 290 300 MEHYKETGYP LAVKLGTITP DGADVYSFDE EEPVLDPHIA KHLAHFGIDM LQMQVAENGL 310 320 330 340 350 360 RDNDIKPRVS EWEVIQEAGV KLKPMYGPGY TGMKNLGNSC YLNAVMQAIF SIPEFQRAYV 370 380 390 400 410 420 GNLPRIFDYS PLDPTQDFNT QMAKLGHGLL SGQYSKPPMK SELIEQVMKE EHKPQQNGIS 430 440 450 460 470 480 PQMFKAFISK DHTEFSSNRQ QDAQEFFLHL INLVERNPVG SENPSDVFRF LVEERTQCCQ 490 500 510 520 530 540 SRKVRYTERV DYIMQLPVAM EAATNKDELI AYELKRREAE AARRAPPELV RAKIPFSACL 550 560 570 580 590 600 QAFSEPTNVE DFWSSALQAK SAGVKTSRFA SFPQYLVVQI KKFTFGLDWI PKKLDVSIDM 610 620 630 640 650 660 PDFLDISHLR AMGLQPGEEE LPDIAPPIII PEDPKDRMMN NFVESLDIDE SSVMQLAEMG 670 680 690 700 710 720 FPLEACRKAV YYTGNLGAEV AFNWIIAHME EPDFAEPLVV PVFGGAASSG VAGLGAVGLD 730 740 750 760 770 780 NQPPEEMVSI IISMGFQRSL AIQALKATNN NLERALEWIF SHPELEEEDG EPALNVMDLE 790 800 810 820 830 840 NHTNANILAE ARSEGPRIKD GPGRYELFGF ISHMGTSTMS GHYVCHLKKE GRWVIYNDLR 850 860 VCASERPPKD LGYIYFYHRI PS

References

[1]

"Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution." Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P., Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B., Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C., Fulton R.S., Graves T.A. , Kremitzki C., Layman D., Magrini V., McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O., Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W., Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D., Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K., Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L., Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K., Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E., Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M., Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M., Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S., Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M., Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S., Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J., Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J., Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E., Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M., Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A., Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M., Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O., Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R., Wilson R.K. Nature 432:695-716(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Red jungle fowl.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AADN02020803 Genomic DNA. No translation available. AADN02020804 Genomic DNA. No translation available. AADN02020805 Genomic DNA. No translation available. AADN02020806 Genomic DNA. No translation available.
IPI	IPI00582057.
RefSeq	XP_426842.2. XM_426842.3.
3D structure databases
ProteinModelPortal	E1BY77.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSGALT00000014487; ENSGALP00000014471; ENSGALG00000008909.
GeneID	429286.
KEGG	gga:429286.
Organism-specific databases
CTD	8975.
Phylogenomic databases
GeneTree	ENSGT00390000000874.
KO	K11836.
OMA	PQQNGIS.
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	20830031.

Entry information

Entry name

UBP13_CHICK

Accession

Primary (citable) accession number: E1BY77

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2012
Last sequence update:	November 2, 2010
Last modified:	April 3, 2013
This is version 25 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program