ORTH5_ARATH
ID ORTH5_ARATH Reviewed; 623 AA.
AC Q680I0; Q6NQ90; Q9C8E0;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=E3 ubiquitin-protein ligase ORTHRUS 5;
DE EC=2.3.2.27;
DE AltName: Full=Protein VARIANT IN METHYLATION 2;
DE AltName: Full=RING-type E3 ubiquitin transferase ORTHRUS 5 {ECO:0000305};
GN Name=ORTH5; Synonyms=VIM2; OrderedLocusNames=At1g66050; ORFNames=F15E12.5;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
RP GENE FAMILY ORGANIZATION.
RX PubMed=11983057; DOI=10.1186/gb-2002-3-4-research0016;
RA Kosarev P., Mayer K.F.X., Hardtke C.S.;
RT "Evaluation and classification of RING-finger domains encoded by the
RT Arabidopsis genome.";
RL Genome Biol. 3:RESEARCH0016.1-RESEARCH0016.12(2002).
RN [6]
RP FUNCTION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18643997; DOI=10.1111/j.1365-313x.2008.03631.x;
RA Kraft E., Bostick M., Jacobsen S.E., Callis J.;
RT "ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin
RT E3 ligases.";
RL Plant J. 56:704-715(2008).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
RX PubMed=18704160; DOI=10.1371/journal.pgen.1000156;
RA Woo H.R., Dittmer T.A., Richards E.J.;
RT "Three SRA-domain methylcytosine-binding proteins cooperate to maintain
RT global CpG methylation and epigenetic silencing in Arabidopsis.";
RL PLoS Genet. 4:E1000156-E1000156(2008).
CC -!- FUNCTION: E3 ubiquitin-protein ligase. Participates in CpG methylation-
CC dependent transcriptional regulation and epigenetic transcriptional
CC silencing. Mediates ubiquitination with the E2 ubiquitin-conjugating
CC enzyme UBC11. {ECO:0000269|PubMed:18643997,
CC ECO:0000269|PubMed:18704160}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00358,
CC ECO:0000269|PubMed:18704160}. Note=Broadly distributed in the nucleus
CC and enriched in the heterochromatic chromocenters.
CC -!- TISSUE SPECIFICITY: Expressed in inflorescences.
CC {ECO:0000269|PubMed:18704160}.
CC -!- DOMAIN: The RING fingers are required for ubiquitin ligase activity.
CC {ECO:0000250}.
CC -!- DOMAIN: The YDG domain mediates the interaction with histone H3.
CC {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Decreased DNA methylation primarily at CpG sites
CC in genic regions, as well as repeated sequences in heterochromatic
CC regions. Released transcriptional silencing at heterochromatin regions.
CC Ectopic CpHpH methylation in the 5S rRNA genes against a background of
CC CpG hypomethylation. {ECO:0000269|PubMed:18704160}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG51305.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAQ65191.1; Type=Miscellaneous discrepancy; Note=Sequencing or cloning errors.; Evidence={ECO:0000305};
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DR EMBL; AC026480; AAG51305.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE34456.1; -; Genomic_DNA.
DR EMBL; BT010568; AAQ65191.1; ALT_SEQ; mRNA.
DR EMBL; AK175694; BAD43457.1; -; mRNA.
DR EMBL; AK175887; BAD43650.1; -; mRNA.
DR EMBL; AK176012; BAD43775.1; -; mRNA.
DR PIR; A96685; A96685.
DR RefSeq; NP_176779.2; NM_105276.4.
DR AlphaFoldDB; Q680I0; -.
DR SMR; Q680I0; -.
DR STRING; 3702.AT1G66050.1; -.
DR BindingDB; Q680I0; -.
DR PaxDb; Q680I0; -.
DR PRIDE; Q680I0; -.
DR EnsemblPlants; AT1G66050.1; AT1G66050.1; AT1G66050.
DR GeneID; 842919; -.
DR Gramene; AT1G66050.1; AT1G66050.1; AT1G66050.
DR KEGG; ath:AT1G66050; -.
DR Araport; AT1G66050; -.
DR TAIR; locus:2013840; AT1G66050.
DR eggNOG; ENOG502QRDQ; Eukaryota.
DR HOGENOM; CLU_016281_0_0_1; -.
DR InParanoid; Q680I0; -.
DR OMA; MAARNIH; -.
DR OrthoDB; 1469576at2759; -.
DR PhylomeDB; Q680I0; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q680I0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q680I0; baseline and differential.
DR Genevisible; Q680I0; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0042393; F:histone binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008327; F:methyl-CpG binding; ISS:UniProtKB.
DR GO; GO:0010428; F:methyl-CpNpG binding; ISS:UniProtKB.
DR GO; GO:0010429; F:methyl-CpNpN binding; ISS:UniProtKB.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:TAIR.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0010216; P:maintenance of DNA methylation; IBA:GO_Central.
DR GO; GO:0090309; P:positive regulation of DNA methylation-dependent heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0016567; P:protein ubiquitination; IDA:TAIR.
DR Gene3D; 2.30.280.10; -; 1.
DR Gene3D; 3.30.40.10; -; 3.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036987; SRA-YDG_sf.
DR InterPro; IPR003105; SRA_YDG.
DR InterPro; IPR045134; UHRF1/2-like.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR027370; Znf-RING_LisH.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR017907; Znf_RING_CS.
DR PANTHER; PTHR14140; PTHR14140; 1.
DR Pfam; PF02182; SAD_SRA; 1.
DR Pfam; PF13445; zf-RING_UBOX; 1.
DR SMART; SM00249; PHD; 1.
DR SMART; SM00184; RING; 2.
DR SMART; SM00466; SRA; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR PROSITE; PS51015; YDG; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS00518; ZF_RING_1; 1.
DR PROSITE; PS50089; ZF_RING_2; 2.
PE 2: Evidence at transcript level;
KW Chromatin regulator; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Transferase; Ubl conjugation pathway; Zinc;
KW Zinc-finger.
FT CHAIN 1..623
FT /note="E3 ubiquitin-protein ligase ORTHRUS 5"
FT /id="PRO_0000396829"
FT DOMAIN 258..407
FT /note="YDG"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00358"
FT ZN_FING 12..62
FT /note="PHD-type"
FT ZN_FING 129..169
FT /note="RING-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT ZN_FING 498..555
FT /note="RING-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 580..623
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 623 AA; 68719 MW; 7BF866893635D2CE CRC64;
MAIQTQLPCD GDGVCMRCQV NPPSEETLTC GTCVTPWHVS CLLPESLASS TGDWECPDCS
GVVVPSAAPG TGISGPESSG SVLVTAIRAI QADVTLTEAE KAKKRQRLMS GGGDDGVDDE
EKKKLEIFCS ICIQLPERPV TTPCGHNFCL KCFEKWAVGQ GKLTCMICRS KIPRHVAKNP
RINLALVSAI RLANVTKCSG EATAAKVHHI IRNQDRPDKA FTTERAVKTG KANAASGKFF
VTIPRDHFGP IPAANDVTRN QGVLVGESWE DRQECRQWGV HFPHVAGIAG QAAVGAQSVA
LSGGYDDDED HGEWFLYTGS GGRDLSGNKR VNKIQSSDQA FKNMNEALRL SCKMGYPVRV
VRSWKEKRSA YAPAEGVRYD GVYRIEKCWS NVGVQGLHKM CRYLFVRCDN EPAPWTSDEH
GDRPRPLPDV PELENATDLF VRKESPSWGF DEAEGRWKWM KSPPVSRMAL DTEERKKNKR
AKKGNNAMKA RLLKEFSCQI CRKVLSLPVT TPCAHNFCKA CLEAKFAGIT QLRDRSNGVR
KLRAKKNIMT CPCCTTDLSE FLQNPQVNRE MMEIIENFKK SEEEAEVAES SNISEEEGEE
ESEPPTKKIK MDKNSVGGTS LSA
