OTU5_ARATH
ID OTU5_ARATH Reviewed; 332 AA.
AC Q9LYC7; A0A178VEN6; A0A178VGH0; B9DF87; Q8W457;
DT 18-SEP-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 5 {ECO:0000303|PubMed:24659992};
DE Short=OTU domain-containing protein 5 {ECO:0000303|PubMed:24659992};
DE EC=3.4.19.12 {ECO:0000250|UniProtKB:Q8N6M0};
DE AltName: Full=Deubiquitinating enzyme OTU5 {ECO:0000303|PubMed:24659992};
GN Name=OTU5 {ECO:0000303|PubMed:24659992};
GN OrderedLocusNames=At3g62940 {ECO:0000312|Araport:AT3G62940};
GN ORFNames=T20O10.40 {ECO:0000312|EMBL:CAB87739.1};
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 AND 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=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 2).
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 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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-302 (ISOFORM 1).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=29061907; DOI=10.1104/pp.17.01188;
RA Yen M.-R., Suen D.-F., Hsu F.-M., Tsai Y.-H., Fu H., Schmidt W.,
RA Chen P.-Y.;
RT "Deubiquitinating enzyme OTU5 contributes to DNA methylation patterns and
RT is critical for phosphate nutrition signals.";
RL Plant Physiol. 175:1826-1838(2017).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=29301952; DOI=10.1104/pp.17.01525;
RA Suen D.-F., Tsai Y.-H., Cheng Y.-T., Radjacommare R., Ahirwar R.N., Fu H.,
RA Schmidt W.;
RT "The deubiquitinase OTU5 regulates root responses to phosphate
RT starvation.";
RL Plant Physiol. 176:2441-2455(2018).
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 (Probable).
CC Inactive cysteine protease (PubMed:24659992). Deubiquitinating enzyme
CC which regulates gene expression by contributing to chromatin
CC organization and DNA methylation patterns (e.g. H3K4me3 and H3K27me3)
CC (PubMed:29061907). Involved in the interpretation of environmental
CC information, probably by altering chromatin organization and
CC maintaining redox homeostasis (PubMed:29301952). Required for phosphate
CC (Pi) homeostasis (e.g. responses upon Pi starvation including DNA
CC methylation and histone methylation) (PubMed:29061907,
CC PubMed:29301952). Negative regulator of root hair morphogenesis
CC (PubMed:29301952). {ECO:0000269|PubMed:24659992,
CC ECO:0000269|PubMed:29061907, ECO:0000269|PubMed:29301952,
CC ECO:0000305|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:0000250|UniProtKB:Q8N6M0};
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=OTU5a {ECO:0000303|PubMed:24659992};
CC IsoId=Q9LYC7-1; Sequence=Displayed;
CC Name=2; Synonyms=OTU5b {ECO:0000303|PubMed:24659992};
CC IsoId=Q9LYC7-2; Sequence=VSP_060260;
CC -!- DISRUPTION PHENOTYPE: Altered DNA methylation of root hair-related
CC genes and altered phosphate (Pi)-responsive root traits
CC (PubMed:29061907). Abnormal responses upon Pi starvation leading to the
CC formation of very short root hairs instead of increased lateral root
CC formation and increased root hair length (PubMed:29061907). On low-Pi
CC media, altered H3K4 and H3K27 trimethylation levels at the
CC transcriptional start site of a subset of genes encoding key players in
CC Pi homeostasis thus leading to a reduced transcription of these genes
CC (PubMed:29061907, PubMed:29301952). Under Pi-replete conditions,
CC constitutive Pi deficiency root phenotype such as attenuated primary
CC root growth associated with increased root hairs development
CC (PubMed:29061907, PubMed:29301952). Accumulation of proteins involved
CC in chromatin remodeling and altered distribution of reactive oxygen
CC species along the root (PubMed:29301952). {ECO:0000269|PubMed:29061907,
CC ECO:0000269|PubMed:29301952}.
CC -!- SIMILARITY: Belongs to the peptidase C85 family. {ECO:0000305}.
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DR EMBL; JQ013449; AFS88952.1; -; mRNA.
DR EMBL; JQ013450; AFS88953.1; -; mRNA.
DR EMBL; AL163816; CAB87739.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80413.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80414.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80415.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM63748.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM63749.1; -; Genomic_DNA.
DR EMBL; AY062840; AAL32918.1; -; mRNA.
DR EMBL; AY081578; AAM10140.1; -; mRNA.
DR EMBL; AY085474; AAM62700.1; -; mRNA.
DR EMBL; AK316676; BAH19404.1; -; mRNA.
DR PIR; T48083; T48083.
DR RefSeq; NP_001190165.1; NM_001203236.2. [Q9LYC7-1]
DR RefSeq; NP_001325819.1; NM_001340186.1. [Q9LYC7-2]
DR RefSeq; NP_001325820.1; NM_001340185.1. [Q9LYC7-1]
DR RefSeq; NP_191853.1; NM_116159.4. [Q9LYC7-1]
DR RefSeq; NP_850739.1; NM_180408.3. [Q9LYC7-2]
DR AlphaFoldDB; Q9LYC7; -.
DR SMR; Q9LYC7; -.
DR IntAct; Q9LYC7; 1.
DR STRING; 3702.AT3G62940.3; -.
DR PaxDb; Q9LYC7; -.
DR PRIDE; Q9LYC7; -.
DR ProteomicsDB; 189452; -.
DR ProteomicsDB; 251890; -. [Q9LYC7-1]
DR EnsemblPlants; AT3G62940.1; AT3G62940.1; AT3G62940. [Q9LYC7-2]
DR EnsemblPlants; AT3G62940.2; AT3G62940.2; AT3G62940. [Q9LYC7-1]
DR EnsemblPlants; AT3G62940.3; AT3G62940.3; AT3G62940. [Q9LYC7-1]
DR EnsemblPlants; AT3G62940.4; AT3G62940.4; AT3G62940. [Q9LYC7-1]
DR EnsemblPlants; AT3G62940.5; AT3G62940.5; AT3G62940. [Q9LYC7-2]
DR GeneID; 825469; -.
DR Gramene; AT3G62940.1; AT3G62940.1; AT3G62940. [Q9LYC7-2]
DR Gramene; AT3G62940.2; AT3G62940.2; AT3G62940. [Q9LYC7-1]
DR Gramene; AT3G62940.3; AT3G62940.3; AT3G62940. [Q9LYC7-1]
DR Gramene; AT3G62940.4; AT3G62940.4; AT3G62940. [Q9LYC7-1]
DR Gramene; AT3G62940.5; AT3G62940.5; AT3G62940. [Q9LYC7-2]
DR KEGG; ath:AT3G62940; -.
DR Araport; AT3G62940; -.
DR TAIR; locus:2099172; AT3G62940.
DR eggNOG; KOG2606; Eukaryota.
DR HOGENOM; CLU_034963_0_0_1; -.
DR InParanoid; Q9LYC7; -.
DR OrthoDB; 1541668at2759; -.
DR PhylomeDB; Q9LYC7; -.
DR PRO; PR:Q9LYC7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LYC7; baseline and differential.
DR GO; GO:0005829; C:cytosol; HDA: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 2: Evidence at transcript level;
KW Alternative splicing; Coiled coil; Hydrolase; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..332
FT /note="OVARIAN TUMOR DOMAIN-containing deubiquitinating
FT enzyme 5"
FT /id="PRO_0000447755"
FT DOMAIN 181..327
FT /note="OTU"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT REGION 1..165
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 25..85
FT /evidence="ECO:0000255"
FT COILED 138..158
FT /evidence="ECO:0000255"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 19..85
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 87..101
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 132..165
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 189
FT /evidence="ECO:0000305"
FT ACT_SITE 192
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q8N6M0"
FT ACT_SITE 320
FT /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT VAR_SEQ 1..16
FT /note="Missing (in isoform 2)"
FT /id="VSP_060260"
SQ SEQUENCE 332 AA; 37362 MW; A3B24F661309D51E CRC64;
MADNKTSEGI VSEETPMDAS QEQQHETVEE MLARHRQEIK QLQNKETEMK KAAAKGSKAE
QKAKKKQVED DISKLSTKLK DKQLKELASQ GFSSSSSNNI AKDETTEKKG DIDTLVRAIA
GVSVTAQQEH SKPSKSVKRR EKRAKEEADR EQRIKEEQSH VKSDRMVENA KLEKKLKPLG
LTVSEIKPDG HCLYRAVENQ LANRSGGASP YTYQNLREMA ASYMREHKTD FLPFFLSETE
GDSNSGSAEE RFEKYCREVE STAAWGSQLE LGALTHCLRK HIKVYSGSFP DVEMGKEYRS
GDDSSLMLSY HRHAFGLGEH YNSVVLVNNI TG
