ORTH2_ARATH
ID ORTH2_ARATH Reviewed; 645 AA.
AC Q8VYZ0; Q3ECM8; Q9FVS3;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=E3 ubiquitin-protein ligase ORTHRUS 2;
DE EC=2.3.2.27;
DE AltName: Full=Protein VARIANT IN METHYLATION 1;
DE AltName: Full=RING-type E3 ubiquitin transferase ORTHRUS 2 {ECO:0000305};
GN Name=ORTH2; Synonyms=VIM1; OrderedLocusNames=At1g57820; ORFNames=F12K22.14;
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] (ISOFORM 2).
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] (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 [4]
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 [5]
RP FUNCTION.
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 [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH CENH3; HTB2; HTR3 AND
RP H4.
RX PubMed=17242155; DOI=10.1101/gad.1512007;
RA Woo H.R., Pontes O., Pikaard C.S., Richards E.J.;
RT "VIM1, a methylcytosine-binding protein required for centromeric
RT heterochromatinization.";
RL Genes Dev. 21:267-277(2007).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, 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 [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 enzyme UBC11. Promotes methylation-mediated gene silencing leading, for
CC example, to early flowering. Associates with methylated DNA, and can
CC bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for
CC methylated forms, and with highest affinity for CpG substrate. Probably
CC acts at the DNA methylation?histone interface to maintain centromeric
CC heterochromatin. {ECO:0000269|PubMed:17239600,
CC ECO:0000269|PubMed:17242155, 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 -!- SUBUNIT: Interacts with histones CENH3, HTB2, HTR3 and H4.
CC {ECO:0000269|PubMed:17242155}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00358,
CC ECO:0000269|PubMed:17242155, ECO:0000269|PubMed:18643997,
CC ECO:0000269|PubMed:18704160}. Note=Broadly distributed in the nucleus
CC and enriched in the heterochromatic chromocenters.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8VYZ0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8VYZ0-2; Sequence=VSP_039618;
CC -!- TISSUE SPECIFICITY: Mostly expressed in inflorescence and, to a lower
CC extent, in leaves. {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: Centromere DNA hypomethylation and centromeric
CC heterochromatin decondensation in interphase. Decreased DNA methylation
CC primarily at CpG sites in genic regions, as well as repeated sequences
CC in heterochromatic regions. Released transcriptional silencing at
CC heterochromatin regions. Ectopic CpHpH methylation in the 5S rRNA genes
CC against a background of CpG hypomethylation.
CC {ECO:0000269|PubMed:18704160}.
CC -!- MISCELLANEOUS: ORTH2 is missing in cv. Bor-4 that exhibit a centromere
CC repeat hypomethylation phenotype.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG29238.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC079732; AAG29238.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE33469.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33470.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59484.1; -; Genomic_DNA.
DR EMBL; AY065438; AAL38879.1; -; mRNA.
DR EMBL; AY117235; AAM51310.1; -; mRNA.
DR PIR; E96612; E96612.
DR RefSeq; NP_001319260.1; NM_001333806.1. [Q8VYZ0-1]
DR RefSeq; NP_176092.2; NM_104576.6. [Q8VYZ0-1]
DR RefSeq; NP_974045.1; NM_202316.2. [Q8VYZ0-2]
DR PDB; 7DUF; X-ray; 2.61 A; A/B=1-63.
DR PDBsum; 7DUF; -.
DR AlphaFoldDB; Q8VYZ0; -.
DR SMR; Q8VYZ0; -.
DR BioGRID; 27382; 1.
DR STRING; 3702.AT1G57820.1; -.
DR PaxDb; Q8VYZ0; -.
DR PRIDE; Q8VYZ0; -.
DR ProteomicsDB; 248668; -. [Q8VYZ0-1]
DR EnsemblPlants; AT1G57820.1; AT1G57820.1; AT1G57820. [Q8VYZ0-1]
DR EnsemblPlants; AT1G57820.2; AT1G57820.2; AT1G57820. [Q8VYZ0-2]
DR EnsemblPlants; AT1G57820.3; AT1G57820.3; AT1G57820. [Q8VYZ0-1]
DR GeneID; 842157; -.
DR Gramene; AT1G57820.1; AT1G57820.1; AT1G57820. [Q8VYZ0-1]
DR Gramene; AT1G57820.2; AT1G57820.2; AT1G57820. [Q8VYZ0-2]
DR Gramene; AT1G57820.3; AT1G57820.3; AT1G57820. [Q8VYZ0-1]
DR KEGG; ath:AT1G57820; -.
DR Araport; AT1G57820; -.
DR TAIR; locus:2009420; AT1G57820.
DR eggNOG; ENOG502QSQ8; Eukaryota.
DR HOGENOM; CLU_016281_0_0_1; -.
DR InParanoid; Q8VYZ0; -.
DR OMA; VTPWHVA; -.
DR OrthoDB; 705927at2759; -.
DR PhylomeDB; Q8VYZ0; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q8VYZ0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8VYZ0; baseline and differential.
DR Genevisible; Q8VYZ0; AT.
DR GO; GO:0010369; C:chromocenter; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IDA:TAIR.
DR GO; GO:0010385; F:double-stranded methylated DNA binding; IDA:TAIR.
DR GO; GO:0042393; F:histone binding; IPI: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:0051301; P:cell division; IDA:TAIR.
DR GO; GO:0006325; P:chromatin organization; IPI:TAIR.
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:0031508; P:pericentric heterochromatin assembly; IMP:TAIR.
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; IPR019787; Znf_PHD-finger.
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; PS50016; ZF_PHD_2; 1.
DR PROSITE; PS00518; ZF_RING_1; 1.
DR PROSITE; PS50089; ZF_RING_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chromatin regulator; Coiled coil;
KW DNA-binding; Metal-binding; Nucleus; Reference proteome; Repeat;
KW Transferase; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..645
FT /note="E3 ubiquitin-protein ligase ORTHRUS 2"
FT /id="PRO_0000396826"
FT DOMAIN 273..422
FT /note="YDG"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00358"
FT ZN_FING 12..63
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 146..185
FT /note="RING-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT ZN_FING 518..575
FT /note="RING-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 96..133
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 599..645
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 583..613
FT /evidence="ECO:0000255"
FT COMPBIAS 96..131
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 605..620
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 622..636
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 334..336
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_039618"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:7DUF"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:7DUF"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:7DUF"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:7DUF"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:7DUF"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:7DUF"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:7DUF"
FT HELIX 49..53
FT /evidence="ECO:0007829|PDB:7DUF"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:7DUF"
SQ SEQUENCE 645 AA; 71467 MW; CD0F58538A2975C5 CRC64;
MARDIQLPCD GDGVCMRCKS NPPPEESLTC GTCVTPWHVS CLSSPPKTLA STLQWHCPDC
SGEIDPLPVS GGATGFESAG SDLVAAIRAI EADESLSTEE KAKMRQRLLS GKGVEEDDEE
EKRKKKGKGK NPNLDVLSAL GDNLMCSFCM QLPERPVTKP CGHNACLKCF EKWMGQGKRT
CGKCRSIIPE KMAKNPRINS SLVAAIRLAK VSKSAAATTS KVFHFISNQD RPDKAFTTER
AKKTGKANAA SGKIYVTIPP DHFGPIPAEN DPVRNQGLLV GESWEDRLEC RQWGAHFPHV
AGIAGQSTYG AQSVALSGGY KDDEDHGEWF LYTGSGGRDL SGNKRTNKEQ SFDQKFEKSN
AALKLSCKLG YPVRVVRSHK EKRSAYAPEE GVRYDGVYRI EKCWRKVGVQ GSFKVCRYLF
VRCDNEPAPW TSDENGDRPR PIPNIPELNM ATDLFERKET PSWDFDEGEG CWKWMKPPPA
SKKSVNVLAP EERKNLRKAI KAAHSNTMRA RLLKEFKCQI CQQVLTLPVT TPCAHNFCKA
CLEAKFAGKT LVRERSTGGR TLRSRKNVLN CPCCPTDISD FLQNPQVNRE VAEVIEKLKT
QEEDTAELED EDEGECSGTT PEEDSEQPKK RIKLDTDATV SATIR
