UBP11_RAT
ID UBP11_RAT Reviewed; 921 AA.
AC Q5D006; F7FEA4; Q0D2L8;
DT 13-APR-2016, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 11;
DE EC=3.4.19.12 {ECO:0000250|UniProtKB:P51784};
DE AltName: Full=Deubiquitinating enzyme 11;
DE AltName: Full=Ubiquitin thioesterase 11;
DE AltName: Full=Ubiquitin-specific-processing protease 11;
GN Name=Usp11 {ECO:0000312|EMBL:AAH90333.1, ECO:0000312|RGD:1303052};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116 {ECO:0000312|EMBL:AAH90333.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000312|EMBL:AAI05614.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain {ECO:0000312|EMBL:AAI05614.1};
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-692, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
RN [5] {ECO:0007744|PDB:4MEM}
RP X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) OF 19-237.
RX PubMed=24724799; DOI=10.1021/bi500116x;
RA Harper S., Gratton H.E., Cornaciu I., Oberer M., Scott D.J., Emsley J.,
RA Dreveny I.;
RT "Structure and catalytic regulatory function of ubiquitin specific protease
RT 11 N-terminal and ubiquitin-like domains.";
RL Biochemistry 53:2966-2978(2014).
CC -!- FUNCTION: Protease that can remove conjugated ubiquitin from target
CC proteins and polyubiquitin chains. Inhibits the degradation of target
CC proteins by the proteasome. Cleaves preferentially 'Lys-6' and 'Lys-
CC 63'-linked ubiquitin chains. Has lower activity with 'Lys-11' and 'Lys-
CC 33'-linked ubiquitin chains, and extremely low activity with 'Lys-27',
CC 'Lys-29' and 'Lys-48'-linked ubiquitin chains (in vitro). Plays a role
CC in the regulation of pathways leading to NF-kappa-B activation. Plays a
CC role in the regulation of DNA repair after double-stranded DNA breaks.
CC Acts as a chromatin regulator via its association with the Polycomb
CC group (PcG) multiprotein PRC1-like complex; may act by deubiquitinating
CC components of the PRC1-like comple. Promotes cell proliferation by
CC deubiquitinating phosphorylated E2F1x. {ECO:0000250|UniProtKB:P51784}.
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; Evidence={ECO:0000250|UniProtKB:P51784};
CC -!- SUBUNIT: Monomer (By similarity). Associated component of the Polycomb
CC group (PcG) multiprotein PRC1-like complex (By similarity). Interacts
CC with RANBP9/RANBPM (By similarity). Interacts with BRCA2 (By
CC similarity). Interacts with CHUK/IKKA (By similarity). Interacts with
CC NFKBIA (By similarity). Interacts with SPRY3, RAE1, MYCBP2/PAM, and
CC KCTD6 (By similarity). {ECO:0000250|UniProtKB:P51784}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P51784}. Cytoplasm
CC {ECO:0000250|UniProtKB:P51784}. Chromosome
CC {ECO:0000250|UniProtKB:P51784}. Note=Predominantly nuclear. Associates
CC with chromatin. {ECO:0000250|UniProtKB:P51784}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000255|PROSITE-
CC ProRule:PRU01035}.
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DR EMBL; AC120727; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH474009; EDL97708.1; -; Genomic_DNA.
DR EMBL; BC090333; AAH90333.1; -; mRNA.
DR EMBL; BC105613; AAI05614.1; -; mRNA.
DR RefSeq; NP_001008861.2; NM_001008861.2.
DR PDB; 4MEM; X-ray; 2.34 A; A/B=19-237.
DR PDBsum; 4MEM; -.
DR AlphaFoldDB; Q5D006; -.
DR SMR; Q5D006; -.
DR STRING; 10116.ENSRNOP00000042897; -.
DR MEROPS; C19.014; -.
DR iPTMnet; Q5D006; -.
DR PhosphoSitePlus; Q5D006; -.
DR jPOST; Q5D006; -.
DR PaxDb; Q5D006; -.
DR PRIDE; Q5D006; -.
DR GeneID; 408217; -.
DR KEGG; rno:408217; -.
DR CTD; 8237; -.
DR RGD; 1303052; Usp11.
DR VEuPathDB; HostDB:ENSRNOG00000009049; -.
DR eggNOG; KOG1870; Eukaryota.
DR HOGENOM; CLU_001060_7_1_1; -.
DR OMA; TGQLVIM; -.
DR OrthoDB; 1283205at2759; -.
DR PhylomeDB; Q5D006; -.
DR TreeFam; TF106276; -.
DR Reactome; R-RNO-5689880; Ub-specific processing proteases.
DR PRO; PR:Q5D006; -.
DR Proteomes; UP000002494; Chromosome X.
DR Proteomes; UP000234681; Chromosome x.
DR Bgee; ENSRNOG00000009049; Expressed in frontal cortex and 20 other tissues.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISO:RGD.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR GO; GO:0001222; F:transcription corepressor binding; ISO:RGD.
DR GO; GO:0016579; P:protein deubiquitination; ISO:RGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; TAS:RGD.
DR Gene3D; 3.30.2230.10; -; 1.
DR InterPro; IPR035927; DUSP-like_sf.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR006615; Pept_C19_DUSP.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR028135; Ub_USP-typ.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF06337; DUSP; 1.
DR Pfam; PF14836; Ubiquitin_3; 1.
DR Pfam; PF00443; UCH; 1.
DR SMART; SM00695; DUSP; 1.
DR SUPFAM; SSF143791; SSF143791; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51283; DUSP; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Chromosome; Cytoplasm; Hydrolase; Nucleus;
KW Phosphoprotein; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..921
FT /note="Ubiquitin carboxyl-terminal hydrolase 11"
FT /id="PRO_0000435845"
FT DOMAIN 28..133
FT /note="DUSP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00613"
FT DOMAIN 257..889
FT /note="USP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 592..697
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 893..921
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 600..622
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 631..664
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 675..697
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 266
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT ACT_SITE 847
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT MOD_RES 194
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P51784"
FT MOD_RES 596
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P51784"
FT MOD_RES 692
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 906
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P51784"
FT HELIX 30..41
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 50..55
FT /evidence="ECO:0007829|PDB:4MEM"
FT HELIX 56..68
FT /evidence="ECO:0007829|PDB:4MEM"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:4MEM"
FT TURN 89..91
FT /evidence="ECO:0007829|PDB:4MEM"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:4MEM"
FT HELIX 109..119
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 138..141
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 146..152
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 155..164
FT /evidence="ECO:0007829|PDB:4MEM"
FT HELIX 170..180
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 189..194
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:4MEM"
FT TURN 210..214
FT /evidence="ECO:0007829|PDB:4MEM"
FT STRAND 220..225
FT /evidence="ECO:0007829|PDB:4MEM"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:4MEM"
SQ SEQUENCE 921 AA; 105239 MW; F0481AB43C394731 CRC64;
MAAVAADPAA AAVPASAEDR ETQPEAMPDL DQQWRQIGNG RERPLRAGES WFLVEKHWYK
QWEAYVKGGD QDASTFPGSI NNSGLFEDQI SWHLRERLVE GDDYVLLPAP AWNYLVSWYG
LKDDQPPIER KVIELPGIRK VEVYPIELLL VQHSDMETAL TIQFSYSDSV DLVLQTAREQ
FLVEPQEDTR LWTKNSEGSL DRLCNTQITL LDACLETGQL VIMETRNKDG TWPSAQLCGM
NNMPDEDEDF QGQPGICGLT NLGNTCFMNS ALQCLSNVPQ LTEYFLNNRY LEELNFRNPL
GMKGELAEAY ADLVKQTWSG YHRSIVPNVF KNKVGHFASQ FLGYQQHDSQ ELLSFLLDGL
HEDLNRVKKK EYVELCNGAG RPDLEVAQEA WQNHKRRNDS VIVDTFHGLF KSTLVCPDCG
NVSVTFDPFC YLSVPLPVCS RRVLEVFFVP MDPRRKPEQH RVVVPKKGNI SDLCVALSTH
TSVAPDKMIV ADVFSHRFYK LYQLEDPLSG ILDRDDIFVY EVTGRIEPVE GSRDDIVVPV
YLRERTPSRD YNNSYYGLIL FGHPLLVSVP RDRFSWEGLY NILMYRLSRY VTKPTSDDDD
GDEKGDENED EDVEDDSSSE EEKEEMSGPT DNDGTQESEQ EQAGTSSGVT GRCPSLLDNS
LHTSQWPPRR RRKQLFTLQT VNSNGTSDRT TSPEEAQTQP YIAMDWEPEM KRRYYDEVEA
EGYVKHDCVG YMLKKNPVQL KECIKLFTTV ETLEKENPWY CSSCKQHQLA TKKLDLWMLP
EVLIIHLKRF SFSKFSREKL DTLVQFPIRD LDFSEFVIKP KNESAPDLYK YDLIAVSNHY
GGMRDGHYTT FACNKDSGQW HYFDDNSVSP VNENQIESKA AYVLFYQRQD VGRRQSQTAS
SETPTSPASS STPNSDIMDV N
