ID C3H19_ARATH Reviewed; 1773 AA.
AC Q9SIV5; F4IKD7; Q8S8E0; Q9SIV4;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2012, sequence version 3.
DT 27-MAR-2024, entry version 125.
DE RecName: Full=Zinc finger CCCH domain-containing protein 19;
DE Short=AtC3H19;
DE AltName: Full=Protein Needed for RDR2-independent DNA methylation;
GN Name=NERD; OrderedLocusNames=At2g16485/At2g16480/At2g16470;
GN ORFNames=F16F14;
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=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 [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 GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=17147637; DOI=10.1111/j.1467-7652.2006.00183.x;
RA Underwood B.A., Vanderhaeghen R., Whitford R., Town C.D., Hilson P.;
RT "Simultaneous high-throughput recombinational cloning of open reading
RT frames in closed and open configurations.";
RL Plant Biotechnol. J. 4:317-324(2006).
RN [4]
RP NOMENCLATURE.
RX PubMed=18221561; DOI=10.1186/1471-2164-9-44;
RA Wang D., Guo Y., Wu C., Yang G., Li Y., Zheng C.;
RT "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.";
RL BMC Genomics 9:44-44(2008).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1281, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR LOCATION,
RP INTERACTION WITH HISTONE H3 AND AGO2, AND DOMAIN PHD.
RC STRAIN=cv. Columbia;
RX PubMed=22940247; DOI=10.1016/j.molcel.2012.07.027;
RA Pontier D., Picart C., Roudier F., Garcia D., Lahmy S., Azevedo J.,
RA Alart E., Laudie M., Karlowski W.M., Cooke R., Colot V., Voinnet O.,
RA Lagrange T.;
RT "NERD, a plant-specific GW protein, defines an additional RNAi-dependent
RT chromatin-based pathway in Arabidopsis.";
RL Mol. Cell 48:121-132(2012).
CC -!- FUNCTION: Plays a central role in integrating RNA silencing and
CC chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine
CC pathway leading to transcriptional gene silencing of specific
CC sequences. Involved in a chromatin-based RNA silencing pathway that
CC encompasses both post-transcriptional gene silencing (PTGS) (e.g. RDR1,
CC RDR6 and AGO2) and transcriptional gene silencing (TGS) (e.g. siRNA-
CC dependent DNA methylation and histone H3) components. Mediates siRNA
CC accumulation at specific chromatin loci. Binds H3K4me0 through its PHD
CC to enforce low levels of H3K4 methylation and gene silencing at a
CC subset of genomic loci. {ECO:0000269|PubMed:22940247}.
CC -!- SUBUNIT: Interacts with unmethylated histone H3 and AGO2. The
CC interaction with AGO2 in required to direct DNA methylation and
CC silencing. {ECO:0000269|PubMed:22940247}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22940247}.
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, mostly in the vasculature
CC and shoot apices of young seedlings. {ECO:0000269|PubMed:22940247}.
CC -!- DOMAIN: The PHD-type zinc finger (599-665) binds to unmethylated
CC histone H3 'Lys-4' (H3K4me0). {ECO:0000269|PubMed:22940247}.
CC -!- DISRUPTION PHENOTYPE: Silencing-deficiency characterized by a lower
CC siRNA accumulation and a transcriptional up-regulation of specific loci
CC that correlates with a local loss of cytosine methylation on DNA and an
CC increased methylation of histone H3 'Lys-4' (e.g. H3K4me2, H3K4me3) and
CC 'Lys-36' (e.g. H3K36me3). {ECO:0000269|PubMed:22940247}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD22293.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.; Evidence={ECO:0000305};
CC Sequence=AAD22314.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.; Evidence={ECO:0000305};
CC Sequence=AAM15362.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.; Evidence={ECO:0000305};
CC Sequence=ABE65448.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007047; AAD22314.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC007047; AAD22293.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC007047; AAM15362.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC06501.1; -; Genomic_DNA.
DR EMBL; DQ446507; ABE65448.1; ALT_SEQ; Genomic_DNA.
DR PIR; F84540; F84540.
DR PIR; G84540; G84540.
DR RefSeq; NP_179241.4; NM_127202.5.
DR AlphaFoldDB; Q9SIV5; -.
DR SMR; Q9SIV5; -.
DR STRING; 3702.Q9SIV5; -.
DR iPTMnet; Q9SIV5; -.
DR PaxDb; 3702-AT2G16485-1; -.
DR ProteomicsDB; 239086; -.
DR EnsemblPlants; AT2G16485.1; AT2G16485.1; AT2G16485.
DR GeneID; 816147; -.
DR Gramene; AT2G16485.1; AT2G16485.1; AT2G16485.
DR KEGG; ath:AT2G16485; -.
DR Araport; AT2G16485; -.
DR TAIR; AT2G16485; NERD.
DR eggNOG; KOG1081; Eukaryota.
DR eggNOG; KOG1862; Eukaryota.
DR eggNOG; KOG1946; Eukaryota.
DR HOGENOM; CLU_236474_0_0_1; -.
DR InParanoid; Q9SIV5; -.
DR OrthoDB; 50760at2759; -.
DR PRO; PR:Q9SIV5; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SIV5; baseline and differential.
DR Genevisible; Q9SIV5; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042393; F:histone binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140766; P:siRNA-mediated post-transcriptional gene silencing; IDA:UniProtKB.
DR CDD; cd19757; Bbox1; 1.
DR CDD; cd00072; GYF; 1.
DR CDD; cd15568; PHD5_NSD; 1.
DR CDD; cd10567; SWIB-MDM2_like; 1.
DR Gene3D; 3.30.1490.40; -; 1.
DR Gene3D; 3.90.70.200; Plus-3 domain; 1.
DR Gene3D; 1.10.245.10; SWIB/MDM2 domain; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR InterPro; IPR003169; GYF.
DR InterPro; IPR035445; GYF-like_dom_sf.
DR InterPro; IPR004343; Plus-3_dom.
DR InterPro; IPR036128; Plus3-like_sf.
DR InterPro; IPR019835; SWIB_domain.
DR InterPro; IPR036885; SWIB_MDM2_dom_sf.
DR InterPro; IPR003121; SWIB_MDM2_domain.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR000571; Znf_CCCH.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR13115; UNCHARACTERIZED; 1.
DR PANTHER; PTHR13115:SF29; ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 19; 1.
DR Pfam; PF02213; GYF; 1.
DR Pfam; PF03126; Plus-3; 1.
DR Pfam; PF02201; SWIB; 1.
DR Pfam; PF00642; zf-CCCH; 1.
DR SMART; SM00444; GYF; 1.
DR SMART; SM00249; PHD; 1.
DR SMART; SM00719; Plus3; 1.
DR SMART; SM00151; SWIB; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 1.
DR SUPFAM; SSF55277; GYF domain; 1.
DR SUPFAM; SSF159042; Plus3-like; 1.
DR SUPFAM; SSF47592; SWIB/MDM2 domain; 1.
DR PROSITE; PS50829; GYF; 1.
DR PROSITE; PS51360; PLUS3; 1.
DR PROSITE; PS51925; SWIB_MDM2; 1.
DR PROSITE; PS50103; ZF_C3H1; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Coiled coil; DNA-binding; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; RNA-mediated gene silencing; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1773
FT /note="Zinc finger CCCH domain-containing protein 19"
FT /id="PRO_0000371978"
FT DOMAIN 801..884
FT /note="SWIB/MDM2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01273"
FT DOMAIN 944..1076
FT /note="Plus3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00693"
FT DOMAIN 1307..1361
FT /note="GYF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00101"
FT ZN_FING 599..665
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 1747..1773
FT /note="C3H1-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT REGION 145..166
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 270..290
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 361..409
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 434..591
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 741..797
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 903..935
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1139..1274
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1409..1469
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1485..1605
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1649..1746
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 196..218
FT /evidence="ECO:0000255"
FT COILED 403..437
FT /evidence="ECO:0000255"
FT MOTIF 581..588
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000250"
FT MOTIF 921..928
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000250"
FT COMPBIAS 145..165
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 361..382
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 434..509
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 510..525
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 526..547
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 548..572
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 750..770
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 903..919
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1163..1187
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1191..1222
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1236..1268
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1494..1605
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1281
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862"
SQ SEQUENCE 1773 AA; 195051 MW; BA42B4F2F2238FB7 CRC64;
MDSDSERASL ESIKDNSECV HVSNEPNLTA TCVDSSVGEE GVTDVNSSAA VSELVPPEQG
EGALLNSVPE ISERGIPVDV VSSVDGGGEE NAAFNIQEID SVGGDAAAVE EVPLKSSSVV
GEGREEEAGA SIVKEEDFVA EANLSGDRLE ENKEVSMEEE PSSHELSVCE VNGVDSLNDE
ENREVGEQIV CGSMGGEEIE SDLESKKEKV DVIEEETTAQ AASLVNAIEI PDDKEVACVA
GFTEISSQDK GLDESGNGFL DEEPVKELQI GEGAKDLTDG DAKEGVDVTE DEMDIQVLKK
SKEEEKVDST TELEIETMRL EVHDVATEMS DKTVISSAVV TQFTGETSND KETVMDDVKE
DVDKDSEAGK SLDIHVPEAT EEVDTDVNYG VGIEKEGDGV GGAEEAGQTV DLEEIREENQ
ELSKELAQVD ETKISEMSEV TETMIKDEDQ EKDDNMTDLA EDVENHRDSS VADIEEGRED
HEDMGVTETQ KETVLGKVDR TKIAEVSEET DTRIEDEDQE KDDEMTDVAE DVKTHGDSSV
ADIEEGRESQ EEMTETQEDS VMADEEPEEV EEENKSAGGK RKRGRNTKTV KGTGKKKEED
VCFMCFDGGD LVLCDRRGCT KAYHPSCVDR DEAFFQTKGK WNCGWHLCSK CEKTATYLCY
TCMFSLCKGC AKDAVFFCIR GNKGLCETCM ETVKLIERKQ QEKEPAQLDF NDKTSWEYLF
KDYWIDLKTQ LSLSPEELDQ AKRPLKGHET NASKQGTASE TDYVTDGGSD SDSSPKKRKT
RSRSKSGSAE KILSSGDKNL SDETMEWASK ELLDLVVHMR RGDRSFLPML EVQTLLLAYI
KRYNLRDPRR KSQVICDSRL QNLFGKSHVG HFEMLNLLDS HFLKKEQNQA DDIQGDIVDT
EEPNHVDVDE NLDHPVKSGK DKKRKTRKKN VRKGRQSNLD DFAAVDMHNI NLIYLRRSLV
EDLLEDSTAF EEKVASAFVR LRISGNQKQD LYRLVQVVGT SKAPEPYKVG KKTTDYVLEI
LNLDKTEVIS IDIISNQDFT EDECKRLKQS IKCGLINRLT VGDIQEKAIA LQEVRVKNLL
EAEILRFSHL RDRASDMGRR KEYPYLLKLS NSLTMLTLRE CVEKLQLLKS PEERQRRLEE
IPEIHADPKM DPDCESEDED EKEEKEKEKQ LRPRSSSFNR RGRDPISPRK GGFSSNESWT
GTSNYSNTSA NRELSRSYSG RGSTGRGDYL GSSDDKVSDS MWTSAREREV QPSLGSEKPR
SVSIPETPAR SSRAIAPPEL SPRIASEISM APPAVVSQPV PKSNDSEKIW HYKDPSGKVQ
GPFSMAQLRK WNNTGYFPAK LEIWKANESP LDSVLLTDAL AGLFQKQTQA VDNSYMKAQV
AAFSGQSSQS EPNLGFAARI APTTIEIPRN SQDTWSQGGS LPSPTPNQIT TPTAKRRNFE
SRWSPTKPSP QSANQSMNYS VAQSGQSQTS RIDIPVVVNS AGALQPQTYP IPTPDPINVS
VNHSATLHSP TPAGGKQSWG SMQTDHGGSN TPSSQNNSTS YGTPSPSVLP SQSQPGFPPS
DSWKVAVPSQ PNAQAQAQWG MNMVNNNQNS AQPQAPANQN SSWGQGTVNP NMGWVGPAQT
GVNVNWGGSS VPSTVQGITH SGWVAPVQGQ TQAYPNPGWG PTGHPQSQSQ SQVQAQAGTT
GSGWMQPGQG IQSGNSNQNW GTQNQTAIPS GGSGGNQAGY WGNQQQSQNG DSGYGWNRQS
GGQQNNFKGQ RVCKFFRENG HCRKGASCNY LHN
//
