IDD5_ARATH
ID IDD5_ARATH Reviewed; 602 AA.
AC Q9ZUL3; Q8RXE0;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Protein indeterminate-domain 5, chloroplastic {ECO:0000303|PubMed:16784536};
DE AltName: Full=ID1-like zinc finger protein 2 {ECO:0000303|Ref.1};
DE Flags: Precursor;
GN Name=IDD5 {ECO:0000303|PubMed:16784536}; Synonyms=IDZ2 {ECO:0000303|Ref.1};
GN OrderedLocusNames=At2g02070 {ECO:0000312|Araport:AT2G02070};
GN ORFNames=F5O4.16 {ECO:0000312|EMBL:AAC97225.1};
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].
RC STRAIN=cv. Columbia;
RA Dewald M., Fritz J., Merkle T.;
RT "INDETERMINATE1-like genes in Arabidopsis.";
RL Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
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 [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].
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-71, 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 [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-60 AND SER-71, AND
RP IDENTIFICATION BY 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, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=22898356; DOI=10.1186/1752-0509-6-100;
RA Ingkasuwan P., Netrphan S., Prasitwattanaseree S., Tanticharoen M.,
RA Bhumiratana S., Meechai A., Chaijaruwanich J., Takahashi H.,
RA Cheevadhanarak S.;
RT "Inferring transcriptional gene regulation network of starch metabolism in
RT Arabidopsis thaliana leaves using graphical Gaussian model.";
RL BMC Syst. Biol. 6:100-100(2012).
RN [10]
RP FUNCTION, AND INTERACTION WITH RGA AND SCL3.
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 acting as a positive regulator of the
CC starch synthase SS4. Controls chloroplast development and starch
CC granule formation (PubMed:22898356). Binds DNA via its zinc fingers
CC (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-
CC AGACAA-3' to promotes its expression when in complex with RGA
CC (PubMed:24821766). {ECO:0000269|PubMed:22898356,
CC ECO:0000269|PubMed:24821766}.
CC -!- SUBUNIT: Binds to RGA and SCL3 competitively.
CC {ECO:0000269|PubMed:24821766}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000305|PubMed:16934950}.
CC -!- TISSUE SPECIFICITY: Highly expressed in leaf tissues.
CC {ECO:0000305|PubMed:22898356}.
CC -!- DISRUPTION PHENOTYPE: Down-regulation of SS4 during the light period of
CC both short and long day conditions. Deformity of the chloroplasts and
CC their contained starch granules, with an increased number of starch
CC granules per chloroplast. {ECO:0000269|PubMed:22898356}.
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DR EMBL; AJ621495; CAF18564.1; -; mRNA.
DR EMBL; AC005936; AAC97225.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05542.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM62239.1; -; Genomic_DNA.
DR EMBL; AY056174; AAL07023.1; -; mRNA.
DR EMBL; BT001215; AAN65102.1; -; mRNA.
DR EMBL; AY081314; AAL91203.1; -; mRNA.
DR PIR; F84432; F84432.
DR RefSeq; NP_001324413.1; NM_001335091.1.
DR RefSeq; NP_178316.1; NM_126268.3.
DR AlphaFoldDB; Q9ZUL3; -.
DR IntAct; Q9ZUL3; 7.
DR STRING; 3702.AT2G02070.1; -.
DR iPTMnet; Q9ZUL3; -.
DR PaxDb; Q9ZUL3; -.
DR PRIDE; Q9ZUL3; -.
DR ProteomicsDB; 228786; -.
DR EnsemblPlants; AT2G02070.1; AT2G02070.1; AT2G02070.
DR EnsemblPlants; AT2G02070.2; AT2G02070.2; AT2G02070.
DR GeneID; 814738; -.
DR Gramene; AT2G02070.1; AT2G02070.1; AT2G02070.
DR Gramene; AT2G02070.2; AT2G02070.2; AT2G02070.
DR KEGG; ath:AT2G02070; -.
DR Araport; AT2G02070; -.
DR TAIR; locus:2051698; AT2G02070.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_014578_3_0_1; -.
DR InParanoid; Q9ZUL3; -.
DR OMA; GMYGESE; -.
DR OrthoDB; 871848at2759; -.
DR PhylomeDB; Q9ZUL3; -.
DR PRO; PR:Q9ZUL3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9ZUL3; baseline and differential.
DR Genevisible; Q9ZUL3; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR InterPro; IPR022755; Znf_C2H2_jaz.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF12171; zf-C2H2_jaz; 1.
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; Chloroplast; DNA-binding; Metal-binding; Phosphoprotein;
KW Plastid; Reference proteome; Repeat; Transcription;
KW Transcription regulation; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..50
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 51..602
FT /note="Protein indeterminate-domain 5, chloroplastic"
FT /id="PRO_0000431541"
FT ZN_FING 81..103
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 122..152
FT /note="C2H2-type 2"
FT /evidence="ECO:0000305"
FT ZN_FING 157..180
FT /note="C2H2-type 2; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 184..207
FT /note="CCHC-type 2; atypical"
FT /evidence="ECO:0000305"
FT REGION 1..65
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 194..206
FT /note="SHR-binding"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT REGION 443..467
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 537..602
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 27..51
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 539..590
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 159
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 162
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="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 186
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
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 201
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 205
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="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 71
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT CONFLICT 30..31
FT /note="AA -> VV (in Ref. 4; AAL91203)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 602 AA; 64464 MW; 843C08FF4CDFA272 CRC64;
MAASSSSAAS FFGVRQDDQS HLLPPNSSAA APPPPPPHHQ APLPPLEAPP QKKKRNQPRT
PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK
VYLCPEPSCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCD KCSKRYAVQS DWKAHSKTCG
TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNNSNNNA
SSMILGLSHM GAPQNLDHQP GDVLRLGSGG GGGGAASRSS SDLIAANASG YFMQEQNPSF
HDQQDHHHHH QQGFLAGNNN IKQSPMSFQQ NLMQFSHDNH NSAPSNVFNL SFLSGNNGVT
SATSNPNAAA AAAVSSGNLM ISNHYDGENA VGGGGEGSTG LFPNNLMSSA DRISSGSVPS
LFSSSMQSPN SAPHMSATAL LQKAAQMGST SSNNNNGSNT NNNNNASSIL RSFGSGIYGE
NESNLQDLMN SFSNPGATGN VNGVDSPFGS YGGVNKGLSA DKQSMTRDFL GVGQIVKSMS
GSGGFQQQQQ QQQQQQQQQQ HGNSRERVGS SSDSADRSSM NVNTGGGPAS TSPPYGIHHA
SF
