IDD9_ARATH
ID IDD9_ARATH Reviewed; 446 AA.
AC Q944L3; Q9M3F1;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Zinc finger protein BALDIBIS {ECO:0000303|PubMed:25829440};
DE AltName: Full=ID1-like zinc finger protein 1 {ECO:0000303|Ref.1};
DE AltName: Full=Protein indeterminate-domain 9 {ECO:0000303|PubMed:16784536};
GN Name=BIB {ECO:0000303|PubMed:25829440};
GN Synonyms=IDD9 {ECO:0000303|PubMed:16784536}, IDZ1 {ECO:0000303|Ref.1};
GN OrderedLocusNames=At3g45260 {ECO:0000312|Araport:AT3G45260};
GN ORFNames=F18N11.20 {ECO:0000312|EMBL:CAB72475.1};
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].
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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].
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 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).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
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, together with JKD, regulates
CC tissue boundaries and asymmetric cell division in roots by a rapid up-
CC regulation of 'SCARECROW' (SCR), thus controlling the nuclear
CC localization of 'SHORT-ROOT' (SHR) and restricting its action
CC (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis
CC initial/daughter (CEI/CEID) tissues (PubMed:25829440). Binds DNA via
CC 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:0000269|PubMed:25829440}.
CC -!- SUBUNIT: Binds to RGA and SCL3 competitively in the nucleus.
CC {ECO:0000269|PubMed:24821766}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, especially in vascular
CC initials, cortex, endodermis, and quiescent center (QC).
CC {ECO:0000269|PubMed:25829440}.
CC -!- DISRUPTION PHENOTYPE: After germination, roots display aberrant
CC divisions in the quiescent center (QC), but normal radial cellular
CC organization. Reduced SCR expression in the quiescent center (QC). The
CC double mutant jkd bib exhibits ectopic divisions in the ground tissue
CC (GT) region leading to an additional layer at the root pole of mature
CC embryos and seedlings, thus resulting in roots with wider meristems and
CC additional layers between the central stele and the epidermis as well
CC as an increased cell number per layer leading to unclear morphological
CC tissue distinctions; in root meristems, only a dynamic subset of layers
CC expresses SCR, restricted to the stele-adjacent layer at the root pole,
CC and specific to ectopic dividing tissues. In the double mutant, SHR
CC accumulates in the expanded inner vascular tissue and in all
CC surrounding cell layers, including epidermis, with inefficient nuclear
CC retention. The quadruple mutant line jkd mgp nuc scr has short root
CC meristems, lacks endodermis and miss Casparian strip.
CC {ECO:0000269|PubMed:25829440}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB72475.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AJ621493; CAF18562.1; -; mRNA.
DR EMBL; AL132953; CAB72475.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78015.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65354.1; -; Genomic_DNA.
DR EMBL; AF428302; AAL16134.1; -; mRNA.
DR EMBL; AY143936; AAN28875.1; -; mRNA.
DR PIR; T47466; T47466.
DR RefSeq; NP_001327332.1; NM_001339201.1.
DR RefSeq; NP_566877.1; NM_114395.4.
DR PDB; 6KPD; X-ray; 3.20 A; B=348-383.
DR PDBsum; 6KPD; -.
DR AlphaFoldDB; Q944L3; -.
DR SMR; Q944L3; -.
DR STRING; 3702.AT3G45260.1; -.
DR iPTMnet; Q944L3; -.
DR PaxDb; Q944L3; -.
DR PRIDE; Q944L3; -.
DR ProteomicsDB; 228790; -.
DR EnsemblPlants; AT3G45260.1; AT3G45260.1; AT3G45260.
DR EnsemblPlants; AT3G45260.2; AT3G45260.2; AT3G45260.
DR GeneID; 823664; -.
DR Gramene; AT3G45260.1; AT3G45260.1; AT3G45260.
DR Gramene; AT3G45260.2; AT3G45260.2; AT3G45260.
DR KEGG; ath:AT3G45260; -.
DR Araport; AT3G45260; -.
DR TAIR; locus:2078262; AT3G45260.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_014578_3_1_1; -.
DR InParanoid; Q944L3; -.
DR OMA; GININRH; -.
DR OrthoDB; 799267at2759; -.
DR PhylomeDB; Q944L3; -.
DR PRO; PR:Q944L3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q944L3; baseline and differential.
DR Genevisible; Q944L3; 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: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 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 3D-structure; Activator; DNA-binding; Metal-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Repeat; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..446
FT /note="Zinc finger protein BALDIBIS"
FT /id="PRO_0000431544"
FT ZN_FING 68..90
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 110..140
FT /note="C2H2-type 2"
FT /evidence="ECO:0000305"
FT ZN_FING 145..168
FT /note="C2H2-type 2; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 172..195
FT /note="CCHC-type 2; atypical"
FT /evidence="ECO:0000305"
FT REGION 20..53
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 182..194
FT /note="SHR-binding"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT REGION 425..446
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 132..139
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 428..446
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 147
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 163
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 167
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 174
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 176
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 189
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT BINDING 193
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q700D2"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8GYC1"
FT HELIX 354..363
FT /evidence="ECO:0007829|PDB:6KPD"
SQ SEQUENCE 446 AA; 49941 MW; 3888BEB4B3AED5A4 CRC64;
MMMPDDHHPL SFPSYVLHQE HIAPNPNPNP NPTSSNSAKR KRNLPGNPDP DAEVIALSPN
SLMTTNRFIC EVCNKGFKRD QNLQLHRRGH NLPWKLKQRT NKEQVKKKVY ICPEKTCVHH
DPARALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVMSDW KAHSKICGTK EYRCDCGTLF
SRKDSFITHR AFCDALAEES ARFVSVPPAP AYLNNALDVE VNHGNINQNH QQRQLNTTSS
QLDQPGFNTN RNNIAFLGQT LPTNVFASSS SPSPRSASDS LQNLWHLQGQ SSHQWLLNEN
NNNNNNILQR GISKNQEEHE MKNVISNGSL FSSEARNNTN NYNQNGGQIA SMSATALLQK
AAQMGSKRSS SSSSNSKTFG LMTSIFNNKQ AENIKTKEVD ERGFTRDFLG VGSQHRSWPL
LMVNHNLPDS SPPASTDGTP TADMNQ
