OTU6_ARATH
ID OTU6_ARATH Reviewed; 505 AA.
AC Q9XIP2; F4IFS7; Q93Z76;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 6 {ECO:0000303|PubMed:24659992};
DE Short=OTU domain-containing protein 6 {ECO:0000303|PubMed:24659992};
DE EC=3.4.19.12 {ECO:0000269|PubMed:21690391};
DE AltName: Full=Deubiquitinating enzyme OTU6 {ECO:0000303|PubMed:24659992};
DE AltName: Full=Otubain-like deubiquitinase 1 {ECO:0000303|PubMed:24659992};
GN Name=OTU6 {ECO:0000303|PubMed:24659992};
GN Synonyms=OTLD1 {ECO:0000303|PubMed:24659992};
GN OrderedLocusNames=At2g27350 {ECO:0000312|Araport:AT2G27350};
GN ORFNames=F12K2.7 {ECO:0000312|EMBL:AEC07979.1};
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] (ISOFORM 2), FUNCTION, GENE FAMILY, AND
RP 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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, INTERACTION WITH
RP LDL1/KDM1C, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=21690391; DOI=10.1073/pnas.1014030108;
RA Krichevsky A., Zaltsman A., Lacroix B., Citovsky V.;
RT "Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone
RT deubiquitinase complexes in plant gene repression.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:11157-11162(2011).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=27999174; DOI=10.1126/scisignal.aaf6767;
RA Keren I., Citovsky V.;
RT "The histone deubiquitinase OTLD1 targets euchromatin to regulate plant
RT growth.";
RL Sci. Signal. 9:RA125-RA125(2016).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=28703681; DOI=10.1080/15592294.2017.1348446;
RA Keren I., Citovsky V.;
RT "Activation of gene expression by histone deubiquitinase OTLD1.";
RL Epigenetics 12:584-590(2017).
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:21690391,
CC PubMed:24659992). Binds chromatin (e.g. nucleosomes and histones) and
CC has enzymatic histone deubiquitinase activity, specific for the H2B
CC histone (PubMed:21690391, PubMed:28703681). Can both repress (e.g.
CC OSR2) and promote (e.g. AN3) the expression of target genes by
CC associating with chromatin, deubiquitinating H2B and regulating its
CC euchromatic histone marks (e.g. H3ac and H3K4me) (PubMed:28703681). In
CC association with LDL1/KDM1C, involved in transcriptional gene
CC repression via histone deubiquitination and demethylation
CC (PubMed:21690391). Promotes the concerted epigenetic regulation and
CC repression (e.g. the removal of euchromatic histone acetylation,
CC ubiquitination, and methylation marks) of a set of genes (e.g. GA20OX,
CC WUS, OSR2, ARL and ABI5) that collectively limit plant growth thus
CC stimulating plant growth and increasing cell size (PubMed:27999174).
CC {ECO:0000269|PubMed:21690391, ECO:0000269|PubMed:27999174,
CC ECO:0000269|PubMed:28703681, ECO:0000303|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:21690391};
CC -!- SUBUNIT: Interacts with KDM1C. {ECO:0000269|PubMed:21690391}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:21690391}. Cytoplasm
CC {ECO:0000269|PubMed:21690391}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=OTLD1b {ECO:0000303|PubMed:24659992};
CC IsoId=Q9XIP2-1; Sequence=Displayed;
CC Name=2; Synonyms=OTLD1a {ECO:0000303|PubMed:24659992};
CC IsoId=Q9XIP2-2; Sequence=VSP_060261;
CC -!- TISSUE SPECIFICITY: Mostly expressed in stems flowers and siliques,
CC and, to a lower extent, in leaves, roots and seedlings.
CC {ECO:0000269|PubMed:27999174}.
CC -!- DISRUPTION PHENOTYPE: Up-regulated expression of GLP2A/GLP5A due to
CC derepression associated with H2B hyperubiquitination of the target
CC chromatin and H3K4 hypermethylation (PubMed:21690391). Abnormal
CC hallmarks of euchromatin including H3 hyperacetylation, H2B
CC monoubiquitination and H3K4 trimethylation in the gene encoding OSR2
CC leading to its increased expression (PubMed:27999174). Repressed
CC expression of the AN3 gene associated with epigenetic modification
CC (e.g. H2B hyperubiquitination and reduced H3ac and H3K4me) of its
CC chromatin (PubMed:28703681). {ECO:0000269|PubMed:21690391,
CC ECO:0000269|PubMed:27999174, ECO:0000269|PubMed:28703681}.
CC -!- SIMILARITY: Belongs to the peptidase C85 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; JQ013451; AFS88954.1; -; mRNA.
DR EMBL; AC006233; AAD41995.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC07979.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07980.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07981.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07984.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07982.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07983.1; -; Genomic_DNA.
DR EMBL; AY058065; AAL24173.1; -; mRNA.
DR EMBL; BT002479; AAO00839.1; -; mRNA.
DR EMBL; BT008876; AAP68315.1; -; mRNA.
DR PIR; H84671; H84671.
DR RefSeq; NP_001189616.1; NM_001202687.2. [Q9XIP2-2]
DR RefSeq; NP_565648.1; NM_128294.2. [Q9XIP2-1]
DR RefSeq; NP_850099.1; NM_179768.4. [Q9XIP2-1]
DR RefSeq; NP_973544.1; NM_201815.2. [Q9XIP2-2]
DR RefSeq; NP_973545.2; NM_201816.5. [Q9XIP2-2]
DR RefSeq; NP_973546.2; NM_201817.2. [Q9XIP2-2]
DR AlphaFoldDB; Q9XIP2; -.
DR SMR; Q9XIP2; -.
DR STRING; 3702.AT2G27350.5; -.
DR MEROPS; C85.001; -.
DR iPTMnet; Q9XIP2; -.
DR ProteomicsDB; 175525; -.
DR ProteomicsDB; 177653; -. [Q9XIP2-1]
DR EnsemblPlants; AT2G27350.1; AT2G27350.1; AT2G27350. [Q9XIP2-1]
DR EnsemblPlants; AT2G27350.2; AT2G27350.2; AT2G27350. [Q9XIP2-1]
DR EnsemblPlants; AT2G27350.3; AT2G27350.3; AT2G27350. [Q9XIP2-2]
DR EnsemblPlants; AT2G27350.4; AT2G27350.4; AT2G27350. [Q9XIP2-2]
DR EnsemblPlants; AT2G27350.5; AT2G27350.5; AT2G27350. [Q9XIP2-2]
DR EnsemblPlants; AT2G27350.6; AT2G27350.6; AT2G27350. [Q9XIP2-2]
DR GeneID; 817278; -.
DR Gramene; AT2G27350.1; AT2G27350.1; AT2G27350. [Q9XIP2-1]
DR Gramene; AT2G27350.2; AT2G27350.2; AT2G27350. [Q9XIP2-1]
DR Gramene; AT2G27350.3; AT2G27350.3; AT2G27350. [Q9XIP2-2]
DR Gramene; AT2G27350.4; AT2G27350.4; AT2G27350. [Q9XIP2-2]
DR Gramene; AT2G27350.5; AT2G27350.5; AT2G27350. [Q9XIP2-2]
DR Gramene; AT2G27350.6; AT2G27350.6; AT2G27350. [Q9XIP2-2]
DR KEGG; ath:AT2G27350; -.
DR Araport; AT2G27350; -.
DR TAIR; locus:2039642; AT2G27350.
DR eggNOG; KOG2605; Eukaryota.
DR HOGENOM; CLU_040365_0_0_1; -.
DR OMA; IQAFCEM; -.
DR OrthoDB; 1448656at2759; -.
DR PhylomeDB; Q9XIP2; -.
DR PRO; PR:Q9XIP2; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9XIP2; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR GO; GO:0042393; F:histone binding; IDA:UniProtKB.
DR GO; GO:0031491; F:nucleosome binding; IDA:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016578; P:histone deubiquitination; IDA:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0045927; P:positive regulation of growth; IMP:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0001558; P:regulation of cell growth; IMP:UniProtKB.
DR GO; GO:1902275; P:regulation of chromatin organization; IMP:UniProtKB.
DR GO; GO:0035065; P:regulation of histone acetylation; IMP:UniProtKB.
DR GO; GO:0031060; P:regulation of histone methylation; IMP:UniProtKB.
DR GO; GO:0033182; P:regulation of histone ubiquitination; IMP:UniProtKB.
DR InterPro; IPR003323; OTU_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR Pfam; PF02338; OTU; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50802; OTU; 1.
DR PROSITE; PS50030; UBA; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Chromatin regulator; Cytoplasm; Hydrolase;
KW Nucleus; Protease; Reference proteome; Repressor; Ubl conjugation pathway.
FT CHAIN 1..505
FT /note="OVARIAN TUMOR DOMAIN-containing deubiquitinating
FT enzyme 6"
FT /id="PRO_0000447756"
FT DOMAIN 216..339
FT /note="OTU"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT DOMAIN 446..491
FT /note="UBA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT REGION 1..191
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 416..447
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..40
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 55..76
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 155..178
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 418..438
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 224
FT /evidence="ECO:0000255"
FT ACT_SITE 227
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q96G74"
FT ACT_SITE 332
FT /evidence="ECO:0000250|UniProtKB:Q96G74"
FT VAR_SEQ 435
FT /note="R -> TG (in isoform 2)"
FT /id="VSP_060261"
SQ SEQUENCE 505 AA; 55274 MW; C53B5D57496BAB66 CRC64;
MTRILVQRGS SGSSSNSSRP SSSSSSSSGS ETQINNNIPV PPVTIDEEIT DEKQEEVTVV
EKAECSDAKD VAVDSDEPAD REDDEGLVVA ENVHVQSEGI DCDSPVSGGS NSDSPPVPAP
PPKPSSTVNP GSNRSVLGSF GALRIGPTRR AAGPRSLVSS RSSPTGSHPS SPRSHSENEG
YNSSDEHMPC YVPSHPGSGL EREHQFEAEI RYSKGFEIRR MLEDGNCLFR AVADQVYGDS
EAYDLARQMC MDYMEQERDH FSQFITEGFT SYLKRKRRDK VYGNNVEIQA LAEMYNRPIH
IYSYSTEPIN IFQGNYSTDT PPIRLSYHHG NHYNSLVDPH RLTVGAGLGF SSLSGRHVDK
EQVKAAIKAQ QEHQIDNALL AEGRFYSDLE LTEKEIERSV MEASRAEYLM EWSKPRIGPK
ESSTSNAETS SSGARPSGSD SKPAEAVKEK TVLSSSIEMV LSMGFSYAQA MEAYSIFGDD
VDSMVCYVLE TSCGGNNRRK GKATE
