IDD15_ARATH
ID IDD15_ARATH Reviewed; 445 AA.
AC F4IPE3; B3H5E9; Q0WVN8; Q2V4B1; Q9ZPT0;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=Zinc finger protein SHOOT GRAVITROPISM 5 {ECO:0000303|PubMed:9210330};
DE AltName: Full=Protein indeterminate-domain 15 {ECO:0000303|PubMed:16784536};
DE Short=AtIDD15 {ECO:0000303|PubMed:16784536};
GN Name=SGR5 {ECO:0000303|PubMed:9210330};
GN Synonyms=IDD15 {ECO:0000303|PubMed:16784536};
GN OrderedLocusNames=At2g01940 {ECO:0000312|Araport:AT2G01940};
GN ORFNames=F14H20.1 {ECO:0000312|EMBL:AAD20087.1};
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=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=9210330; DOI=10.1093/oxfordjournals.pcp.a029201;
RA Yamauchi Y., Fukaki H., Fujisawa H., Tasaka M.;
RT "Mutations in the SGR4, SGR5 and SGR6 loci of Arabidopsis thaliana alter
RT the shoot gravitropism.";
RL Plant Cell Physiol. 38:530-535(1997).
RN [6]
RP GENE FAMILY.
RX PubMed=15236668; DOI=10.1186/1471-2164-5-39;
RA Englbrecht C.C., Schoof H., Boehm S.;
RT "Conservation, diversification and expansion of C2H2 zinc finger proteins
RT in the Arabidopsis thaliana genome.";
RL BMC Genomics 5:39-39(2004).
RN [7]
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 [8]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ASP-165, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=16813575; DOI=10.1111/j.1365-313x.2006.02807.x;
RA Morita M.T., Sakaguchi K., Kiyose S., Taira K., Kato T., Nakamura M.,
RA Tasaka M.;
RT "A C2H2-type zinc finger protein, SGR5, is involved in early events of
RT gravitropism in Arabidopsis inflorescence stems.";
RL Plant J. 47:619-628(2006).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=18259878; DOI=10.1007/s11103-008-9301-0;
RA Tanimoto M., Tremblay R., Colasanti J.;
RT "Altered gravitropic response, amyloplast sedimentation and circumnutation
RT in the Arabidopsis shoot gravitropism 5 mutant are associated with reduced
RT starch levels.";
RL Plant Mol. Biol. 67:57-69(2008).
RN [10]
RP FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, AND INDUCTION BY AUXIN.
RX PubMed=24039602; DOI=10.1371/journal.pgen.1003759;
RA Cui D., Zhao J., Jing Y., Fan M., Liu J., Wang Z., Xin W., Hu Y.;
RT "The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral
RT organ morphogenesis and gravitropism by promoting auxin biosynthesis and
RT transport.";
RL PLoS Genet. 9:E1003759-E1003759(2013).
CC -!- FUNCTION: Transcription factor involved in inflorescence stems
CC gravitropism, probably by regulating starch accumulation in amyloplasts
CC of graviperceptive cells. Required for stem circumnutation movements.
CC Regulates lateral organ morphogenesis and gravitropic responses
CC (PubMed:24039602). Acts cooperatively with IDD16 to control silique and
CC branche orientation (PubMed:24039602). Involved in the establishment of
CC auxin gradients through the regulation of auxin biosynthesis and
CC transport (PubMed:24039602). {ECO:0000269|PubMed:16813575,
CC ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602,
CC ECO:0000269|PubMed:9210330}.
CC -!- INTERACTION:
CC F4IPE3; B9DHT4: ARIA; NbExp=3; IntAct=EBI-15192881, EBI-15192195;
CC F4IPE3; F4JI72: At4g03250; NbExp=4; IntAct=EBI-15192881, EBI-15192535;
CC F4IPE3; Q8L925: CRC; NbExp=3; IntAct=EBI-15192881, EBI-15197527;
CC F4IPE3; Q9C9X7: IDD14; NbExp=5; IntAct=EBI-15192881, EBI-15191579;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16813575}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=F4IPE3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4IPE3-2; Sequence=VSP_054698;
CC Name=3;
CC IsoId=F4IPE3-3; Sequence=VSP_054699;
CC -!- TISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-
CC sensing tissue in inflorescence stems. Mostly present in stems and
CC flowers, and, to a lower extent, in seedlings, hypocotyls, roots and
CC the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
CC -!- DEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in
CC both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
CC -!- INDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
CC -!- DISRUPTION PHENOTYPE: In sgr5-2 and sgr5-3, abnormal inflorescence
CC stems gravitropism but normal hypocotyl and root gravitropism. Slow
CC amyloplasts sedimentation associated with lower amyloplast starch
CC levels. Attenuated stem circumnutation movement. No visible phenotype
CC (PubMed:24039602). {ECO:0000269|PubMed:16813575,
CC ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602,
CC ECO:0000269|PubMed:9210330}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD20087.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BX819715; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC006532; AAD20087.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002685; AEC05523.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05524.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05525.1; -; Genomic_DNA.
DR EMBL; BX819715; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK226703; BAE98810.1; -; mRNA.
DR PIR; A84431; A84431.
DR RefSeq; NP_001030949.2; NM_001035872.3. [F4IPE3-2]
DR RefSeq; NP_001077868.1; NM_001084399.1. [F4IPE3-3]
DR RefSeq; NP_178303.2; NM_126255.4. [F4IPE3-1]
DR AlphaFoldDB; F4IPE3; -.
DR BioGRID; 128; 18.
DR IntAct; F4IPE3; 17.
DR STRING; 3702.AT2G01940.3; -.
DR PaxDb; F4IPE3; -.
DR PRIDE; F4IPE3; -.
DR ProteomicsDB; 228780; -. [F4IPE3-1]
DR EnsemblPlants; AT2G01940.1; AT2G01940.1; AT2G01940. [F4IPE3-1]
DR EnsemblPlants; AT2G01940.2; AT2G01940.2; AT2G01940. [F4IPE3-2]
DR EnsemblPlants; AT2G01940.3; AT2G01940.3; AT2G01940. [F4IPE3-3]
DR GeneID; 814725; -.
DR Gramene; AT2G01940.1; AT2G01940.1; AT2G01940. [F4IPE3-1]
DR Gramene; AT2G01940.2; AT2G01940.2; AT2G01940. [F4IPE3-2]
DR Gramene; AT2G01940.3; AT2G01940.3; AT2G01940. [F4IPE3-3]
DR KEGG; ath:AT2G01940; -.
DR Araport; AT2G01940; -.
DR TAIR; locus:2041105; AT2G01940.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_014578_0_1_1; -.
DR OrthoDB; 1318335at2759; -.
DR PRO; PR:F4IPE3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4IPE3; baseline and differential.
DR Genevisible; F4IPE3; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0010031; P:circumnutation; IMP:TAIR.
DR GO; GO:0009590; P:detection of gravity; IMP:TAIR.
DR GO; GO:0048444; P:floral organ morphogenesis; IGI:TAIR.
DR GO; GO:0009630; P:gravitropism; IGI:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IGI:TAIR.
DR GO; GO:0009959; P:negative gravitropism; IMP:TAIR.
DR GO; GO:0010601; P:positive regulation of auxin biosynthetic process; IGI:TAIR.
DR GO; GO:2000012; P:regulation of auxin polar transport; IGI:TAIR.
DR GO; GO:2000904; P:regulation of starch metabolic process; IMP:TAIR.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR InterPro; IPR039288; SGR5-like.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR PANTHER; PTHR34946; PTHR34946; 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 Alternative splicing; Coiled coil; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Repeat; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..445
FT /note="Zinc finger protein SHOOT GRAVITROPISM 5"
FT /id="PRO_0000429060"
FT ZN_FING 73..95
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 115..145
FT /note="C2H2-type 2"
FT /evidence="ECO:0000305"
FT ZN_FING 151..178
FT /note="C2H2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 178..201
FT /note="CCHC-type 2; atypical"
FT /evidence="ECO:0000305"
FT REGION 22..59
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 188..200
FT /note="SHR-binding"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT REGION 203..253
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 281..314
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 340..397
FT /evidence="ECO:0000255"
FT COMPBIAS 22..46
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 216..244
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 153
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 156
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 169
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 173
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 182
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 199
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT VAR_SEQ 1..89
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.4"
FT /id="VSP_054698"
FT VAR_SEQ 184..187
FT /note="RVFS -> FFSSF (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_054699"
FT MUTAGEN 165
FT /note="D->N: In sgr5-1; weak gravitropic responses in
FT inflorescence stems."
FT /evidence="ECO:0000269|PubMed:16813575"
FT CONFLICT 139
FT /note="K -> G (in Ref. 3; BX819715)"
FT /evidence="ECO:0000305"
FT CONFLICT 150
FT /note="Q -> R (in Ref. 3; BX819715)"
FT /evidence="ECO:0000305"
FT CONFLICT 155
FT /note="R -> S (in Ref. 3; BX819715)"
FT /evidence="ECO:0000305"
FT CONFLICT 230
FT /note="S -> R (in Ref. 3; BX819715)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 445 AA; 50140 MW; C310B37E9376AC60 CRC64;
MRTDQVMLSN KNTNTCCVVS SSSSDPFLSS SENGVTTTNT STQKRKRRPA GTPDPDAEVV
SLSPRTLLES DRYICEICNQ GFQRDQNLQM HRRRHKVPWK LLKRDNNIEV KKRVYVCPEP
TCLHHNPCHA LGDLVGIKKH FRRKHSNHKQ WVCERCSKGY AVQSDYKAHL KTCGTRGHSC
DCGRVFSRVE SFIEHQDNCS ARRVHREPPR PPQTAVTVPA CSSRTASTVS TPSSETNYGG
TVAVTTPQPL EGRPIHQRIS SSILTNSSNN LNLELQLLPL SSNQNPNQEN QQQKVKEPSH
HHNHNHDTTN LNLSIAPSSS YQHYNNFDRI KEIMASEQIM KIAMKEKAYA EEAKREAKRQ
REIAENEFAN AKKIRQKAQA ELERAKFLKE QSMKKISSTI MQVTCQTCKG QFQAVAVPAA
TADETSLVVS YMSSANTDGE LENGF
