ORTH1_ARATH
ID ORTH1_ARATH Reviewed; 617 AA.
AC Q9FKA7; Q67XP0;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=E3 ubiquitin-protein ligase ORTHRUS 1;
DE EC=2.3.2.27;
DE AltName: Full=Protein VARIANT IN METHYLATION 3;
DE AltName: Full=RING-type E3 ubiquitin transferase ORTHRUS 1 {ECO:0000305};
GN Name=ORTH1; Synonyms=VIM3; OrderedLocusNames=At5g39550; ORFNames=MIJ24.3;
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=9734815; DOI=10.1093/dnares/5.3.203;
RA Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence
RT features of the regions of 1,367,185 bp covered by 19 physically assigned
RT P1 and TAC clones.";
RL DNA Res. 5:203-216(1998).
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 (MAR-2005) 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, AND MUTAGENESIS OF SER-292 AND ARG-362.
RX PubMed=17239600; DOI=10.1016/j.cub.2007.01.009;
RA Johnson L.M., Bostick M., Zhang X., Kraft E., Henderson I., Callis J.,
RA Jacobsen S.E.;
RT "The SRA methyl-cytosine-binding domain links DNA and histone
RT methylation.";
RL Curr. Biol. 17:379-384(2007).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, RING FINGER FUNCTION, GENE FAMILY, AND
RP 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 [8]
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 enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and
CC UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. Promotes
CC methylation-mediated gene silencing leading, for example, to early
CC flowering. Can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong
CC preference for methylated forms, and with highest affinity for CpG
CC substrate. {ECO:0000269|PubMed:17239600, 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:18643997, ECO:0000269|PubMed:18704160}. Note=Broadly
CC distributed in the nucleus and enriched in the heterochromatic
CC chromocenters.
CC -!- TISSUE SPECIFICITY: Expressed in inflorescences and leaves.
CC {ECO:0000269|PubMed:18704160}.
CC -!- DOMAIN: The RING fingers are required for ubiquitin ligase activity.
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}.
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DR EMBL; AB012243; BAB08886.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94446.1; -; Genomic_DNA.
DR EMBL; BT010573; AAQ65196.1; -; mRNA.
DR EMBL; AK176778; BAD44541.1; -; mRNA.
DR EMBL; AK221256; BAD93904.1; -; mRNA.
DR RefSeq; NP_198771.1; NM_123317.4.
DR AlphaFoldDB; Q9FKA7; -.
DR SMR; Q9FKA7; -.
DR STRING; 3702.AT5G39550.1; -.
DR iPTMnet; Q9FKA7; -.
DR PaxDb; Q9FKA7; -.
DR PRIDE; Q9FKA7; -.
DR ProteomicsDB; 248667; -.
DR EnsemblPlants; AT5G39550.1; AT5G39550.1; AT5G39550.
DR GeneID; 833951; -.
DR Gramene; AT5G39550.1; AT5G39550.1; AT5G39550.
DR KEGG; ath:AT5G39550; -.
DR Araport; AT5G39550; -.
DR TAIR; locus:2164835; AT5G39550.
DR eggNOG; ENOG502QRDQ; Eukaryota.
DR HOGENOM; CLU_016281_0_0_1; -.
DR InParanoid; Q9FKA7; -.
DR OMA; SICAASW; -.
DR OrthoDB; 705927at2759; -.
DR PhylomeDB; Q9FKA7; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q9FKA7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FKA7; baseline and differential.
DR Genevisible; Q9FKA7; 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; IDA:TAIR.
DR GO; GO:0010428; F:methyl-CpNpG binding; IDA:TAIR.
DR GO; GO:0010429; F:methyl-CpNpN binding; IDA:TAIR.
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:0032776; P:DNA methylation on cytosine; IMP:TAIR.
DR GO; GO:0010424; P:DNA methylation on cytosine within a CG sequence; IMP:UniProtKB.
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 GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP: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 1: Evidence at protein level;
KW Chromatin regulator; Coiled coil; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Transferase; Ubl conjugation pathway; Zinc;
KW Zinc-finger.
FT CHAIN 1..617
FT /note="E3 ubiquitin-protein ligase ORTHRUS 1"
FT /id="PRO_0000396825"
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 495..552
FT /note="RING-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 575..617
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 563..593
FT /evidence="ECO:0000255"
FT MUTAGEN 292
FT /note="S->F: Loss of DNA binding activity."
FT /evidence="ECO:0000269|PubMed:17239600"
FT MUTAGEN 362
FT /note="R->H: Loss of DNA binding activity."
FT /evidence="ECO:0000269|PubMed:17239600"
FT CONFLICT 439
FT /note="L -> Q (in Ref. 4; BAD44541)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 617 AA; 68299 MW; 1CAA1ECD2750A165 CRC64;
MAIETQLPCD GDGVCMRCQV NPPSEETLTC GTCVTPWHVP CLLPESLASS TGEWECPDCS
GVVVPSAAPG TGNARPESSG SVLVAAIRAI QADETLTEAE KAKKRQKLMS GGGDDGVDEE
EKKKLEIFCS ICIQLPERPI TTPCGHNFCL KCFEKWAVGQ GKLTCMICRS KIPRHVAKNP
RINLALVSAI RLANVTKCSV EATAAKVHHI IRNQDRPEKA FTTERAVKTG KANAASGKFF
VTIPRDHFGP IPAENDVTRK QGVLVGESWE DRQECRQWGA HFPHIAGIAG QSAVGAQSVA
LSGGYDDDED HGEWFLYTGS GGRDLSGNKR INKKQSSDQA FKNMNESLRL SCKMGYPVRV
VRSWKEKRSA YAPAEGVRYD GVYRIEKCWS NVGVQGSFKV CRYLFVRCDN EPAPWTSDEH
GDRPRPLPNV PELETAADLF VRKESPSWDF DEAEGRWKWM KSPPVSRMAL DPEERKKNKR
AKNTMKARLL KEFSCQICRE VLSLPVTTPC AHNFCKACLE AKFAGITQLR ERSNGGRKLR
AKKNIMTCPC CTTDLSEFLQ NPQVNREMME IIENFKKSEE EADASISEEE EEESEPPTKK
IKMDNNSVGG SGTSLSA
