OTU4_ARATH
ID OTU4_ARATH Reviewed; 317 AA.
AC Q8LBZ4; A0A178VJL7; A0A2H1ZEL0; K9M8R2; K9M8T1; K9M8Y0; K9M9G5; Q67XW3;
AC Q682S6; Q9M2R6;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 4 {ECO:0000303|PubMed:24659992};
DE Short=OTU domain-containing protein 4 {ECO:0000303|PubMed:24659992};
DE EC=3.4.19.12 {ECO:0000269|PubMed:24659992};
DE AltName: Full=Deubiquitinating enzyme OTU4 {ECO:0000303|PubMed:24659992};
GN Name=OTU4 {ECO:0000303|PubMed:24659992};
GN OrderedLocusNames=At3g57810 {ECO:0000312|Araport:AT3G57810};
GN ORFNames=T10K17.20 {ECO:0000312|EMBL:CAB67609.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 4 AND 5), FUNCTION, MUTAGENESIS
RP OF CYS-179, BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, GENE FAMILY,
RP AND NOMENCLATURE.
RX PubMed=24659992; DOI=10.3389/fpls.2014.00084;
RA Radjacommare R., Usharani R., Kuo C.-H., Fu H.;
RT "Distinct phylogenetic relationships and biochemical properties of
RT Arabidopsis ovarian tumor-related deubiquitinases support their functional
RT differentiation.";
RL Front. Plant Sci. 5:84-84(2014).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kim C.J., Chen H., Quinitio C., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP PREDICTION.
RX PubMed=15333753; DOI=10.1104/pp.104.043695;
RA Reumann S., Ma C., Lemke S., Babujee L.;
RT "AraPerox. A database of putative Arabidopsis proteins from plant
RT peroxisomes.";
RL Plant Physiol. 136:2587-2608(2004).
CC -!- FUNCTION: Hydrolase that can remove conjugated ubiquitin from proteins
CC in vitro and may therefore play an important regulatory role at the
CC level of protein turnover by preventing degradation (PubMed:24659992).
CC Cysteine protease with a preference for 'Lys-63' over 'Lys-48'-linked
CC over 'Met-1' ubiquitin (UB) tetramers (e.g. Ub3 and Ub4) as substrates
CC (PubMed:24659992). Cleaves also RUB-GST fusion (PubMed:24659992).
CC {ECO:0000269|PubMed:24659992}.
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:0000269|PubMed:24659992};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7. {ECO:0000269|PubMed:24659992};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. Note=Prediction of a
CC peroxisomal location. {ECO:0000269|PubMed:15333753}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1; Synonyms=OTU4a {ECO:0000303|PubMed:24659992};
CC IsoId=Q8LBZ4-1; Sequence=Displayed;
CC Name=2; Synonyms=OTU4c {ECO:0000303|PubMed:24659992};
CC IsoId=Q8LBZ4-2; Sequence=VSP_040634;
CC Name=3; Synonyms=OTU4b {ECO:0000303|PubMed:24659992};
CC IsoId=Q8LBZ4-3; Sequence=VSP_060257, VSP_060258;
CC Name=4; Synonyms=OTU4d {ECO:0000303|PubMed:24659992};
CC IsoId=Q8LBZ4-4; Sequence=VSP_040634, VSP_060256, VSP_060259;
CC Name=5; Synonyms=OTU4e {ECO:0000303|PubMed:24659992};
CC IsoId=Q8LBZ4-5; Sequence=VSP_060254, VSP_060255;
CC -!- SIMILARITY: Belongs to the peptidase C65 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD42988.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BAD44468.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BX824976; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAB67609.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; JQ013445; AFS88948.1; -; mRNA.
DR EMBL; JQ013446; AFS88949.1; -; mRNA.
DR EMBL; JQ013447; AFS88950.1; -; mRNA.
DR EMBL; JQ013448; AFS88951.1; -; mRNA.
DR EMBL; AL132977; CAB67609.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE79704.2; -; Genomic_DNA.
DR EMBL; CP002686; AEE79705.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79706.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64743.1; -; Genomic_DNA.
DR EMBL; AY086909; AAM63953.1; -; mRNA.
DR EMBL; BX824976; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK175291; BAD43054.1; -; mRNA.
DR EMBL; AK175225; BAD42988.1; ALT_FRAME; mRNA.
DR EMBL; AK176705; BAD44468.1; ALT_FRAME; mRNA.
DR EMBL; BT026114; ABG48470.1; -; mRNA.
DR PIR; T46003; T46003.
DR RefSeq; NP_001078307.1; NM_001084838.2. [Q8LBZ4-1]
DR RefSeq; NP_001319786.1; NM_001339892.1. [Q8LBZ4-3]
DR RefSeq; NP_001326751.1; NM_001339893.1. [Q8LBZ4-1]
DR RefSeq; NP_850716.1; NM_180385.3. [Q8LBZ4-1]
DR AlphaFoldDB; Q8LBZ4; -.
DR SMR; Q8LBZ4; -.
DR STRING; 3702.AT3G57810.2; -.
DR PaxDb; Q8LBZ4; -.
DR PRIDE; Q8LBZ4; -.
DR ProteomicsDB; 218642; -.
DR ProteomicsDB; 248848; -. [Q8LBZ4-1]
DR EnsemblPlants; AT3G57810.1; AT3G57810.1; AT3G57810. [Q8LBZ4-3]
DR EnsemblPlants; AT3G57810.2; AT3G57810.2; AT3G57810. [Q8LBZ4-1]
DR EnsemblPlants; AT3G57810.3; AT3G57810.3; AT3G57810. [Q8LBZ4-1]
DR EnsemblPlants; AT3G57810.4; AT3G57810.4; AT3G57810. [Q8LBZ4-1]
DR GeneID; 824950; -.
DR Gramene; AT3G57810.1; AT3G57810.1; AT3G57810. [Q8LBZ4-3]
DR Gramene; AT3G57810.2; AT3G57810.2; AT3G57810. [Q8LBZ4-1]
DR Gramene; AT3G57810.3; AT3G57810.3; AT3G57810. [Q8LBZ4-1]
DR Gramene; AT3G57810.4; AT3G57810.4; AT3G57810. [Q8LBZ4-1]
DR KEGG; ath:AT3G57810; -.
DR Araport; AT3G57810; -.
DR TAIR; locus:2095748; AT3G57810.
DR eggNOG; KOG2606; Eukaryota.
DR HOGENOM; CLU_046927_0_0_1; -.
DR InParanoid; Q8LBZ4; -.
DR OMA; VRQIREP; -.
DR OrthoDB; 1448656at2759; -.
DR PhylomeDB; Q8LBZ4; -.
DR PRO; PR:Q8LBZ4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8LBZ4; baseline and differential.
DR Genevisible; Q8LBZ4; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IBA:GO_Central.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR InterPro; IPR003323; OTU_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR Pfam; PF02338; OTU; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50802; OTU; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Hydrolase; Reference proteome;
KW Ubl conjugation pathway.
FT CHAIN 1..317
FT /note="OVARIAN TUMOR DOMAIN-containing deubiquitinating
FT enzyme 4"
FT /id="PRO_0000405233"
FT DOMAIN 168..306
FT /note="OTU"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT ACT_SITE 176
FT /evidence="ECO:0000255"
FT ACT_SITE 179
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q96G74"
FT ACT_SITE 299
FT /evidence="ECO:0000250|UniProtKB:Q96G74"
FT VAR_SEQ 73..115
FT /note="Missing (in isoform 2 and isoform 4)"
FT /evidence="ECO:0000303|Ref.6"
FT /id="VSP_040634"
FT VAR_SEQ 73..75
FT /note="SVL -> CDC (in isoform 5)"
FT /id="VSP_060254"
FT VAR_SEQ 76..317
FT /note="Missing (in isoform 5)"
FT /id="VSP_060255"
FT VAR_SEQ 213..238
FT /note="VADEFIQRRQETEWFVEGDFDTYVRQ -> TGNRMVRGRRFRHLRQTNSGST
FT RVGR (in isoform 4)"
FT /id="VSP_060256"
FT VAR_SEQ 214..217
FT /note="ADEF -> SIYG (in isoform 3)"
FT /id="VSP_060257"
FT VAR_SEQ 218..317
FT /note="Missing (in isoform 3)"
FT /id="VSP_060258"
FT VAR_SEQ 239..317
FT /note="Missing (in isoform 4)"
FT /id="VSP_060259"
FT MUTAGEN 179
FT /note="C->S: Abolished cleavage activities for 'Lys-
FT 48'- and 'Lys-63'-linked ubiquitin (UB) tetramers and of
FT linear UB polymer and RUB-GST fusion."
FT /evidence="ECO:0000269|PubMed:24659992"
FT CONFLICT 123
FT /note="V -> I (in Ref. 5; BX824976)"
FT /evidence="ECO:0000305"
FT CONFLICT 180
FT /note="L -> F (in Ref. 5; BX824976)"
FT /evidence="ECO:0000305"
FT CONFLICT 189..192
FT /note="CLRS -> LLT (in Ref. 5; BX824976)"
FT /evidence="ECO:0000305"
FT CONFLICT 203
FT /note="R -> K (in Ref. 5; BX824976)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 317 AA; 35774 MW; 2A7CBF0649407920 CRC64;
MMICYSPITT CSRNAISIKR HLGSRLYGVV AHGSSKFSCY SLLSGLSRRH YTGFRVSVSN
RPSSWHDKGL FGSVLINRPT VAPKEKLEVS FLSPEANMKC SKIESNMRNL YCYSRFAYTG
VIVSLLVCYS STSQSAYADS SRDKDANNVH HHSSDGKFHN GKRVYTDYSI IGIPGDGRCL
FRSVAHGFCL RSGKLAPGEK MQRELADELR TRVADEFIQR RQETEWFVEG DFDTYVRQIR
DPHVWGGEPE LFMASHVLQM PITVYMKDDK AGGLISIAEY GQEYGKDDPI RVLYHGFGHY
DALLLHESKA SIPKSKL
