UBP13_CHICK
ID UBP13_CHICK Reviewed; 862 AA.
AC E1BY77;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2010, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 13;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 13;
DE AltName: Full=Ubiquitin thioesterase 13;
DE AltName: Full=Ubiquitin-specific-processing protease 13;
GN Name=USP13;
OS Gallus gallus (Chicken).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC Phasianinae; Gallus.
OX NCBI_TaxID=9031;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Red jungle fowl;
RX PubMed=15592404; DOI=10.1038/nature03154;
RA Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B.,
RA Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W.,
RA Yang S.-P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D.,
RA Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K.,
RA Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L.,
RA Crooijmans R.P., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B.,
RA Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M.,
RA Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
RA Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
RA Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
RA Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M.,
RA Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.-S.,
RA Wang J., Liu B., Wang J., Yu J., Yang H., Nefedov M., Koriabine M.,
RA Dejong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M.,
RA Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A.,
RA Elnitski L., Eswara P., King D.C., Yang S.-P., Tyekucheva S.,
RA Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.,
RA Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J.,
RA Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E.,
RA Eichler E., Bao Z., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M.,
RA Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A.,
RA Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
RA Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
RA Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J., Betran E.,
RA Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S.,
RA Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E.,
RA Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R.,
RA Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R.,
RA Wilson R.K.;
RT "Sequence and comparative analysis of the chicken genome provide unique
RT perspectives on vertebrate evolution.";
RL Nature 432:695-716(2004).
CC -!- FUNCTION: Deubiquitinase that mediates deubiquitination of target
CC proteins and is involved in various processes such as autophagy and
CC endoplasmic reticulum-associated degradation (ERAD).
CC {ECO:0000250|UniProtKB:Q92995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12;
CC -!- ACTIVITY REGULATION: Specifically inhibited by spautin-1 (specific and
CC potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13
CC and inhibits deubiquitinase activity. {ECO:0000250}.
CC -!- DOMAIN: The UBP-type zinc finger has lost its ability to bind ubiquitin
CC and USP13 is not activated by unanchored ubiquitin. {ECO:0000250}.
CC -!- DOMAIN: The UBA domains mediate binding to ubiquitin. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AADN02020803; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AADN02020804; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AADN02020805; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AADN02020806; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; E1BY77; -.
DR SMR; E1BY77; -.
DR STRING; 9031.ENSGALP00000014471; -.
DR PaxDb; E1BY77; -.
DR PRIDE; E1BY77; -.
DR VEuPathDB; HostDB:geneid_429286; -.
DR eggNOG; KOG0944; Eukaryota.
DR HOGENOM; CLU_009884_1_0_1; -.
DR InParanoid; E1BY77; -.
DR OrthoDB; 556111at2759; -.
DR PhylomeDB; E1BY77; -.
DR TreeFam; TF300576; -.
DR Proteomes; UP000000539; Unplaced.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:1904288; F:BAT3 complex binding; IEA:Ensembl.
DR GO; GO:0051087; F:chaperone binding; IEA:Ensembl.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR GO; GO:1990380; F:Lys48-specific deubiquitinase activity; IEA:Ensembl.
DR GO; GO:0070628; F:proteasome binding; IEA:Ensembl.
DR GO; GO:0043130; F:ubiquitin binding; ISS:UniProtKB.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IEA:Ensembl.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006914; P:autophagy; IEA:UniProtKB-KW.
DR GO; GO:0008283; P:cell population proliferation; ISS:UniProtKB.
DR GO; GO:1904378; P:maintenance of unfolded protein involved in ERAD pathway; IEA:Ensembl.
DR GO; GO:1904294; P:positive regulation of ERAD pathway; IEA:Ensembl.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0035523; P:protein K29-linked deubiquitination; IEA:Ensembl.
DR GO; GO:0044313; P:protein K6-linked deubiquitination; IEA:Ensembl.
DR GO; GO:0070536; P:protein K63-linked deubiquitination; ISS:UniProtKB.
DR GO; GO:0050821; P:protein stabilization; ISS:UniProtKB.
DR GO; GO:0010506; P:regulation of autophagy; ISS:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR016652; Ubiquitinyl_hydrolase.
DR InterPro; IPR041432; UBP13_Znf-UBP_var.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR001607; Znf_UBP.
DR Pfam; PF00627; UBA; 2.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR Pfam; PF17807; zf-UBP_var; 1.
DR PIRSF; PIRSF016308; UBP; 1.
DR SMART; SM00165; UBA; 2.
DR SMART; SM00290; ZnF_UBP; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50030; UBA; 2.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
PE 3: Inferred from homology;
KW Autophagy; Hydrolase; Metal-binding; Protease; Reference proteome; Repeat;
KW Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..862
FT /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT /id="PRO_0000418012"
FT DOMAIN 331..860
FT /note="USP"
FT DOMAIN 647..688
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 722..762
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT ZN_FING 182..290
FT /note="UBP-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT ACT_SITE 340
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 822
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT BINDING 206
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 209
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 226
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 239
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
SQ SEQUENCE 862 AA; 96649 MW; 9207A3B6846A1018 CRC64;
MQRAALFGGG DAQMAAGDLG ELLVPYMPTI RVPKSGDRVY KTECAFSYDS PDSEGGLYVC
MNTFLGFGRE HIERHYRKTG QCVYLHLKRH VIEKVPGASG GALPKRRNAK LFLDLEANGD
LSSDDFEYED EAKLVIFPDH YEISLPNIEE LPALVTIASD ALLSAKSPYR KQDPDSWEEE
LQASKHAKSL VQLDNGVRIP PSGWKCSKCD LRENLWLNLT DGSVLCGKWF FDGSGGNGHA
MEHYKETGYP LAVKLGTITP DGADVYSFDE EEPVLDPHIA KHLAHFGIDM LQMQVAENGL
RDNDIKPRVS EWEVIQEAGV KLKPMYGPGY TGMKNLGNSC YLNAVMQAIF SIPEFQRAYV
GNLPRIFDYS PLDPTQDFNT QMAKLGHGLL SGQYSKPPMK SELIEQVMKE EHKPQQNGIS
PQMFKAFISK DHTEFSSNRQ QDAQEFFLHL INLVERNPVG SENPSDVFRF LVEERTQCCQ
SRKVRYTERV DYIMQLPVAM EAATNKDELI AYELKRREAE AARRAPPELV RAKIPFSACL
QAFSEPTNVE DFWSSALQAK SAGVKTSRFA SFPQYLVVQI KKFTFGLDWI PKKLDVSIDM
PDFLDISHLR AMGLQPGEEE LPDIAPPIII PEDPKDRMMN NFVESLDIDE SSVMQLAEMG
FPLEACRKAV YYTGNLGAEV AFNWIIAHME EPDFAEPLVV PVFGGAASSG VAGLGAVGLD
NQPPEEMVSI IISMGFQRSL AIQALKATNN NLERALEWIF SHPELEEEDG EPALNVMDLE
NHTNANILAE ARSEGPRIKD GPGRYELFGF ISHMGTSTMS GHYVCHLKKE GRWVIYNDLR
VCASERPPKD LGYIYFYHRI PS
