IDD3_ARATH
ID IDD3_ARATH Reviewed; 506 AA.
AC Q9ZWA6; Q700E8;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Zinc finger protein MAGPIE {ECO:0000303|PubMed:17785527};
DE AltName: Full=Protein POLLEN SPECIFIC GENE 3 {ECO:0000305};
DE AltName: Full=Protein indeterminate-domain 3 {ECO:0000303|PubMed:16784536};
DE Short=AtIDD3 {ECO:0000303|PubMed:24821766};
GN Name=MGP {ECO:0000303|PubMed:17785527};
GN Synonyms=IDD3 {ECO:0000303|PubMed:16784536}, PSG3 {ECO:0000305};
GN OrderedLocusNames=At1g03840 {ECO:0000312|Araport:AT1G03840};
GN ORFNames=F11M21.23 {ECO:0000312|EMBL:AAD10684.1};
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 [MRNA] (ISOFORM 2).
RX PubMed=15208423; DOI=10.1104/pp.104.042176;
RA Gong W., Shen Y.-P., Ma L.-G., Pan Y., Du Y.-L., Wang D.-H., Yang J.-Y.,
RA Hu L.-D., Liu X.-F., Dong C.-X., Ma L., Chen Y.-H., Yang X.-Y., Gao Y.,
RA Zhu D., Tan X., Mu J.-Y., Zhang D.-B., Liu Y.-L., Dinesh-Kumar S.P., Li Y.,
RA Wang X.-P., Gu H.-Y., Qu L.-J., Bai S.-N., Lu Y.-T., Li J.-Y., Zhao J.-D.,
RA Zuo J., Huang H., Deng X.-W., Zhu Y.-X.;
RT "Genome-wide ORFeome cloning and analysis of Arabidopsis transcription
RT factor genes.";
RL Plant Physiol. 135:773-782(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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 [3]
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 [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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
RP INDUCTION BY SHR.
RX PubMed=16640459; DOI=10.1371/journal.pbio.0040143;
RA Levesque M.P., Vernoux T., Busch W., Cui H., Wang J.Y., Blilou I.,
RA Hassan H., Nakajima K., Matsumoto N., Lohmann J.U., Scheres B.,
RA Benfey P.N.;
RT "Whole-genome analysis of the SHORT-ROOT developmental pathway in
RT Arabidopsis.";
RL PLoS Biol. 4:739-752(2006).
RN [8]
RP FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP SHR; SCR AND JKD.
RX PubMed=17785527; DOI=10.1101/gad.440307;
RA Welch D., Hassan H., Blilou I., Immink R., Heidstra R., Scheres B.;
RT "Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric
RT cell division and stabilize tissue boundaries by restricting SHORT-ROOT
RT action.";
RL Genes Dev. 21:2196-2204(2007).
RN [9]
RP DISRUPTION PHENOTYPE.
RX PubMed=21265895; DOI=10.1111/j.1365-313x.2010.04432.x;
RA Seo P.J., Ryu J., Kang S.K., Park C.M.;
RT "Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription
RT factor contributes to photoperiodic flowering in Arabidopsis.";
RL Plant J. 65:418-429(2011).
RN [10]
RP INTERACTION WITH SIEL.
RX PubMed=21924907; DOI=10.1016/j.cub.2011.08.013;
RA Koizumi K., Wu S., MacRae-Crerar A., Gallagher K.L.;
RT "An essential protein that interacts with endosomes and promotes movement
RT of the SHORT-ROOT transcription factor.";
RL Curr. Biol. 21:1559-1564(2011).
RN [11]
RP FUNCTION, AND INDUCTION.
RX PubMed=21935722; DOI=10.1007/s11103-011-9826-5;
RA Ogasawara H., Kaimi R., Colasanti J., Kozaki A.;
RT "Activity of transcription factor JACKDAW is essential for SHR/SCR-
RT dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal
RT interactions with MAGPIE, SCARECROW and SHORT ROOT.";
RL Plant Mol. Biol. 77:489-499(2011).
RN [12]
RP FUNCTION, INTERACTION WITH SCL3 AND RGA, 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).
RN [13]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=25829440; DOI=10.1105/tpc.114.132407;
RA Long Y., Smet W., Cruz-Ramirez A., Castelijns B., de Jonge W.,
RA Maehoenen A.P., Bouchet B.P., Perez G.S., Akhmanova A., Scheres B.,
RA Blilou I.;
RT "Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries
RT by confining the cell fate regulator SHORT-ROOT and contributing to fate
RT specification.";
RL Plant Cell 27:1185-1199(2015).
CC -!- FUNCTION: Transcription factor that regulates tissue boundaries and
CC asymmetric cell division (PubMed:17785527, PubMed:25829440).
CC Contributes to the sequestration of 'SHORT-ROOT' to the nucleus
CC (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP
CC promoters (PubMed:21935722). Does not show transcription activity by
CC itself, but regulates the transcription of downstream genes through
CC interaction with other transcription factors (PubMed:21935722). Binds
CC DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to
CC SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in
CC complex with RGA (PubMed:24821766). Positively involved in gibberellic
CC acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527,
CC ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766,
CC ECO:0000269|PubMed:25829440}.
CC -!- SUBUNIT: Interacts with SHR, SCR and JKD, but not with itself
CC (PubMed:17785527). Interacts with SIEL (PubMed:21924907). Binds to RGA
CC and SCL3 competitively in the nucleus (PubMed:24821766).
CC {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21924907,
CC ECO:0000269|PubMed:24821766}.
CC -!- INTERACTION:
CC Q9ZWA6; Q700D2: JKD; NbExp=3; IntAct=EBI-1568600, EBI-1568562;
CC Q9ZWA6; Q9SN22: SCL32; NbExp=3; IntAct=EBI-1568600, EBI-15196807;
CC Q9ZWA6; Q9M384: SCR; NbExp=3; IntAct=EBI-1568600, EBI-1250484;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:24821766}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9ZWA6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9ZWA6-2; Sequence=VSP_036332;
CC -!- TISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of
CC embryos and 2-days post-germination roots but not in the quiescent
CC center (PubMed:17785527). Detected only in cells that perform
CC asymmetric cell divisions (PubMed:17785527). In roots, present in
CC cortex, endodermis, and pericycle layer (PubMed:25829440).
CC {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
CC -!- INDUCTION: Up-regulated by the transcription factor JKD, and down-
CC regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:21265895,
CC PubMed:25829440). Roots of the triple mutant jkd mgp nuc contain
CC patches of undivided ground tissue (GT), indicating that cortex and
CC endodermis layers are not fully separated. The quadruple mutant line
CC jkd mgp nuc scr has short root meristems, lacks endodermis and miss
CC Casparian strip (PubMed:25829440). {ECO:0000269|PubMed:21265895,
CC ECO:0000269|PubMed:25829440}.
CC -!- MISCELLANEOUS: MGP expression is SHR- and SCR-dependent.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
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DR EMBL; AY568648; AAS79538.1; -; mRNA.
DR EMBL; AJ630476; CAG25849.1; -; mRNA.
DR EMBL; AC003027; AAD10684.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27620.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27621.1; -; Genomic_DNA.
DR EMBL; BT006209; AAP12858.1; -; mRNA.
DR EMBL; AK227837; BAE99815.1; -; mRNA.
DR PIR; A86169; A86169.
DR RefSeq; NP_001030951.1; NM_001035874.1. [Q9ZWA6-2]
DR RefSeq; NP_171880.1; NM_100263.4. [Q9ZWA6-1]
DR AlphaFoldDB; Q9ZWA6; -.
DR BioGRID; 24631; 6.
DR IntAct; Q9ZWA6; 7.
DR STRING; 3702.AT1G03840.1; -.
DR iPTMnet; Q9ZWA6; -.
DR PaxDb; Q9ZWA6; -.
DR PRIDE; Q9ZWA6; -.
DR ProteomicsDB; 228784; -. [Q9ZWA6-1]
DR EnsemblPlants; AT1G03840.1; AT1G03840.1; AT1G03840. [Q9ZWA6-1]
DR EnsemblPlants; AT1G03840.2; AT1G03840.2; AT1G03840. [Q9ZWA6-2]
DR GeneID; 839396; -.
DR Gramene; AT1G03840.1; AT1G03840.1; AT1G03840. [Q9ZWA6-1]
DR Gramene; AT1G03840.2; AT1G03840.2; AT1G03840. [Q9ZWA6-2]
DR KEGG; ath:AT1G03840; -.
DR Araport; AT1G03840; -.
DR TAIR; locus:2024193; AT1G03840.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_014578_3_1_1; -.
DR InParanoid; Q9ZWA6; -.
DR PhylomeDB; Q9ZWA6; -.
DR PRO; PR:Q9ZWA6; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9ZWA6; baseline and differential.
DR Genevisible; Q9ZWA6; AT.
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:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0008356; P:asymmetric cell division; IMP:TAIR.
DR GO; GO:0009740; P:gibberellic acid mediated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0009939; P:positive regulation of gibberellic acid mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0034504; P:protein localization to nucleus; IMP:UniProtKB.
DR GO; GO:0010075; P:regulation of meristem growth; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR GO; GO:0048364; P:root development; IGI:TAIR.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
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; DNA-binding;
KW Gibberellin signaling pathway; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..506
FT /note="Zinc finger protein MAGPIE"
FT /id="PRO_0000337841"
FT ZN_FING 70..92
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 111..141
FT /note="C2H2-type 2"
FT /evidence="ECO:0000305"
FT ZN_FING 146..169
FT /note="C2H2-type 2; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 173..196
FT /note="CCHC-type 2; atypical"
FT /evidence="ECO:0000305"
FT REGION 1..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 183..195
FT /note="SHR-binding"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT MOTIF 133..140
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 1..20
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 21..39
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 148
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 151
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 168
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 175
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 177
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 194
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT MOD_RES 60
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8GYC1"
FT VAR_SEQ 50..51
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15208423"
FT /id="VSP_036332"
SQ SEQUENCE 506 AA; 55826 MW; C27006B44C77D1C7 CRC64;
MTTEDQTISS SGGYVQSSST TDHVDHHHHD QHESLNPPLV KKKRNLPGNP DPEAEVIALS
PKTLMATNRF LCEICGKGFQ RDQNLQLHRR GHNLPWKLKQ RTSKEVRKRV YVCPEKSCVH
HHPTRALGDL TGIKKHFCRK HGEKKWKCEK CAKRYAVQSD WKAHSKTCGT REYRCDCGTI
FSRRDSFITH RAFCDALAEE TARLNAASHL KSFAATAGSN LNYHYLMGTL IPSPSLPQPP
SFPFGPPQPQ HHHHHQFPIT TNNFDHQDVM KPASTLSLWS GGNINHHQQV TIEDRMAPQP
HSPQEDYNWV FGNANNHGEL ITTSDSLITH DNNINIVQSK ENANGATSLS VPSLFSSVDQ
ITQDANAASV AVANMSATAL LQKAAQMGAT SSTSPTTTIT TDQSAYLQSF ASKSNQIVED
GGSDRFFASF GSNSVELMSN NNNGLHEIGN PRNGVTVVSG MGELQNYPWK RRRVDIGNAG
GGGQTRDFLG VGVQTICHSS SINGWI
