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C3H19_ARATH
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   25-MAY-2022, entry version 117.
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.AT2G16485.1; -.
DR   iPTMnet; Q9SIV5; -.
DR   PaxDb; Q9SIV5; -.
DR   PRIDE; Q9SIV5; -.
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; locus:2827287; AT2G16485.
DR   eggNOG; KOG1081; Eukaryota.
DR   eggNOG; KOG1862; Eukaryota.
DR   eggNOG; KOG1946; Eukaryota.
DR   HOGENOM; CLU_236474_0_0_1; -.
DR   InParanoid; Q9SIV5; -.
DR   OrthoDB; 85697at2759; -.
DR   PRO; PR:Q9SIV5; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q9SIV5; baseline and differential.
DR   Genevisible; Q9SIV5; AT.
DR   GO; GO:0016593; C:Cdc73/Paf1 complex; IBA:GO_Central.
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:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IBA:GO_Central.
DR   GO; GO:0032776; P:DNA methylation on cytosine; IMP:UniProtKB.
DR   GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR   GO; GO:0010964; P:regulation of heterochromatin assembly by small RNA; IDA:UniProtKB.
DR   CDD; cd00072; GYF; 1.
DR   Gene3D; 1.10.245.10; -; 1.
DR   Gene3D; 3.30.1490.40; -; 1.
DR   Gene3D; 3.30.40.10; -; 1.
DR   Gene3D; 3.90.70.200; -; 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   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; SSF159042; SSF159042; 1.
DR   SUPFAM; SSF47592; SSF47592; 1.
DR   SUPFAM; SSF55277; SSF55277; 1.
DR   SUPFAM; SSF57903; SSF57903; 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
 
 
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