IDD4_ARATH
ID IDD4_ARATH Reviewed; 516 AA.
AC Q8GYC1; Q9ZUL4;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Protein indeterminate-domain 4, chloroplastic {ECO:0000303|PubMed:16784536};
DE Flags: Precursor;
GN Name=IDD4 {ECO:0000303|PubMed:16784536};
GN OrderedLocusNames=At2g02080 {ECO:0000312|Araport:AT2G02080};
GN ORFNames=F5O4.15 {ECO:0000312|EMBL:BAC42382.1};
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 MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
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 [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16784536; DOI=10.1186/1471-2164-7-158;
RA Colasanti J., Tremblay R., Wong A.Y., Coneva V., Kozaki A., Mable B.K.;
RT "The maize INDETERMINATE1 flowering time regulator defines a highly
RT conserved zinc finger protein family in higher plants.";
RL BMC Genomics 7:158-158(2006).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=16934950; DOI=10.1016/j.gene.2006.06.022;
RA Wagner R., Pfannschmidt T.;
RT "Eukaryotic transcription factors in plastids--Bioinformatic assessment and
RT implications for the evolution of gene expression machineries in plants.";
RL Gene 381:62-70(2006).
RN [7]
RP INDUCTION BY GIBBERELLIN.
RX PubMed=17933900; DOI=10.1105/tpc.107.054999;
RA Zentella R., Zhang Z.L., Park M., Thomas S.G., Endo A., Murase K.,
RA Fleet C.M., Jikumaru Y., Nambara E., Kamiya Y., Sun T.P.;
RT "Global analysis of della direct targets in early gibberellin signaling in
RT Arabidopsis.";
RL Plant Cell 19:3037-3057(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-73, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [9]
RP FUNCTION.
RX PubMed=19726569; DOI=10.1104/pp.109.145987;
RA Kakizaki T., Matsumura H., Nakayama K., Che F.S., Terauchi R., Inaba T.;
RT "Coordination of plastid protein import and nuclear gene expression by
RT plastid-to-nucleus retrograde signaling.";
RL Plant Physiol. 151:1339-1353(2009).
RN [10]
RP FUNCTION, INTERACTION WITH RGA AND SCL3, AND SUBCELLULAR LOCATION.
RX PubMed=24821766; DOI=10.1073/pnas.1321669111;
RA Yoshida H., Hirano K., Sato T., Mitsuda N., Nomoto M., Maeo K., Koketsu E.,
RA Mitani R., Kawamura M., Ishiguro S., Tada Y., Ohme-Takagi M., Matsuoka M.,
RA Ueguchi-Tanaka M.;
RT "DELLA protein functions as a transcriptional activator through the DNA
RT binding of the indeterminate domain family proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:7861-7866(2014).
CC -!- FUNCTION: Transcription factor that may act a transcriptional activator
CC of nuclear-encoded photosynthetic gene expression (Probable). Binds DNA
CC via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3
CC promoter sequence 5'-AGACAA-3' to promotes its expression when in
CC complex with RGA (PubMed:24821766). {ECO:0000269|PubMed:24821766,
CC ECO:0000305|PubMed:19726569}.
CC -!- SUBUNIT: Binds to RGA and SCL3 competitively in the nucleus.
CC {ECO:0000269|PubMed:24821766}.
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Plastid, chloroplast
CC {ECO:0000305|PubMed:16934950}.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Nucleus {ECO:0000255|PROSITE-
CC ProRule:PRU00768, ECO:0000269|PubMed:24821766}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8GYC1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8GYC1-2; Sequence=VSP_057328;
CC -!- INDUCTION: Down-regulated by gibberellin.
CC {ECO:0000305|PubMed:17933900}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC005936; AAC97227.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05543.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05544.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63310.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63311.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63312.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63313.1; -; Genomic_DNA.
DR EMBL; AK117733; BAC42382.1; -; mRNA.
DR EMBL; BT005897; AAO64832.1; -; mRNA.
DR PIR; G84432; G84432.
DR RefSeq; NP_001118254.1; NM_001124782.1. [Q8GYC1-2]
DR RefSeq; NP_001318178.1; NM_001335092.1. [Q8GYC1-2]
DR RefSeq; NP_001325405.1; NM_001335094.1. [Q8GYC1-1]
DR RefSeq; NP_001325406.1; NM_001335093.1. [Q8GYC1-1]
DR RefSeq; NP_001325407.1; NM_001335095.1. [Q8GYC1-1]
DR RefSeq; NP_178317.2; NM_126269.3. [Q8GYC1-1]
DR AlphaFoldDB; Q8GYC1; -.
DR STRING; 3702.AT2G02080.1; -.
DR iPTMnet; Q8GYC1; -.
DR PaxDb; Q8GYC1; -.
DR PRIDE; Q8GYC1; -.
DR ProteomicsDB; 228785; -. [Q8GYC1-1]
DR EnsemblPlants; AT2G02080.1; AT2G02080.1; AT2G02080. [Q8GYC1-1]
DR EnsemblPlants; AT2G02080.2; AT2G02080.2; AT2G02080. [Q8GYC1-2]
DR EnsemblPlants; AT2G02080.3; AT2G02080.3; AT2G02080. [Q8GYC1-1]
DR EnsemblPlants; AT2G02080.4; AT2G02080.4; AT2G02080. [Q8GYC1-1]
DR EnsemblPlants; AT2G02080.5; AT2G02080.5; AT2G02080. [Q8GYC1-1]
DR EnsemblPlants; AT2G02080.6; AT2G02080.6; AT2G02080. [Q8GYC1-2]
DR GeneID; 814739; -.
DR Gramene; AT2G02080.1; AT2G02080.1; AT2G02080. [Q8GYC1-1]
DR Gramene; AT2G02080.2; AT2G02080.2; AT2G02080. [Q8GYC1-2]
DR Gramene; AT2G02080.3; AT2G02080.3; AT2G02080. [Q8GYC1-1]
DR Gramene; AT2G02080.4; AT2G02080.4; AT2G02080. [Q8GYC1-1]
DR Gramene; AT2G02080.5; AT2G02080.5; AT2G02080. [Q8GYC1-1]
DR Gramene; AT2G02080.6; AT2G02080.6; AT2G02080. [Q8GYC1-2]
DR KEGG; ath:AT2G02080; -.
DR Araport; AT2G02080; -.
DR TAIR; locus:2051688; AT2G02080.
DR eggNOG; KOG1721; Eukaryota.
DR InParanoid; Q8GYC1; -.
DR OrthoDB; 871848at2759; -.
DR PhylomeDB; Q8GYC1; -.
DR PRO; PR:Q8GYC1; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8GYC1; baseline and differential.
DR Genevisible; Q8GYC1; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0008356; P:asymmetric cell division; IMP:TAIR.
DR GO; GO:0002221; P:pattern recognition receptor signaling pathway; IMP:TAIR.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR SMART; SM00355; ZnF_C2H2; 3.
DR SUPFAM; SSF57667; SSF57667; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Chloroplast; DNA-binding; Metal-binding;
KW Nucleus; Phosphoprotein; Plastid; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Transit peptide; Zinc;
KW Zinc-finger.
FT TRANSIT 1..70
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 71..516
FT /note="Protein indeterminate-domain 4, chloroplastic"
FT /id="PRO_0000431540"
FT ZN_FING 83..105
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 124..154
FT /note="C2H2-type 2"
FT /evidence="ECO:0000305"
FT ZN_FING 159..182
FT /note="C2H2-type 2; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 186..209
FT /note="CCHC-type 2; atypical"
FT /evidence="ECO:0000305"
FT REGION 1..68
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 196..208
FT /note="SHR-binding"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT REGION 483..516
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 146..153
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 1..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 161
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 181
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 188
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 207
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT MOD_RES 73
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT VAR_SEQ 1..77
FT /note="Missing (in isoform 2)"
FT /id="VSP_057328"
SQ SEQUENCE 516 AA; 55794 MW; 32667E70A2B5AC1B CRC64;
MSSSSYNTSV IPSSSSSAQP FFITSSGTGD NDFNRKDTFM SMIQQPNSSA PPPKKRRNQP
GNPNPDAEVV ALSPKTLMAT NRFICDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK
RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT
CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMTAASS GVGSGGIYGR
LGGGSALSHH HLSDHPNFGF NPLVGYNLNI ASSDNRRDFI PQSSNPNFLI QSASSQGMLN
TTPNNNNQSF MNQHGLIQFD PVDNINLKSS GTNNSFFNLG FFQENTKNSE TSLPSLYSTD
VLVHHREENL NAGSNVSATA LLQKATQMGS VTSNDPSALF RGLASSSNSS SVIANHFGGG
RIMENDNNGN LQGLMNSLAA VNGGGGSGGS IFDVQFGDNG NMSGSDKLTL DFLGVGGMVR
NVNRGGGGGG RGSARGGVSL DGEAKFPEQN YPFGRG
