IDEF1_ORYSJ
ID IDEF1_ORYSJ Reviewed; 362 AA.
AC Q6Z1Z3; A0A0P0XAM4; A9JTY5;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=B3 domain-containing protein IDEF1;
DE AltName: Full=Protein IRON DEFICIENCY-RESPONSIVE ELEMENT FACTOR 1;
GN Name=IDEF1; OrderedLocusNames=Os08g0101000, LOC_Os08g01090;
GN ORFNames=B1147B12.12, OsJ_25718;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP IDENTIFICATION, FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Nipponbare;
RX PubMed=18025467; DOI=10.1073/pnas.0707010104;
RA Kobayashi T., Ogo Y., Nakanishi Itai R., Nakanishi H., Takahashi M.,
RA Mori S., Nishizawa N.K.;
RT "The transcription factor IDEF1 regulates the response to and tolerance of
RT iron deficiency in plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:19150-19155(2007).
RN [7]
RP INDUCTION, AND UBIQUITINATION.
RX PubMed=27137867; DOI=10.1038/srep25485;
RA Tan S., Liu F., Pan X.X., Zang Y.P., Jin F., Zu W.X., Qi X.T., Xiao W.,
RA Yin L.P.;
RT "CSN6, a subunit of the COP9 signalosome, is involved in early response to
RT iron deficiency in Oryza sativa.";
RL Sci. Rep. 6:25485-25485(2016).
CC -!- FUNCTION: Transcription regulator involved in iron deficiency response
CC and tolerance. May regulate directly iron transporters or other
CC transcription factors involved in iron-deficiency response. Binds
CC specifically to the DNA sequence 5'-CATGC-3' of the IDE1 element found
CC in the promoter of the barley iron deficiency-inducible gene IDS2.
CC {ECO:0000269|PubMed:18025467}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00326,
CC ECO:0000269|PubMed:18025467}.
CC -!- TISSUE SPECIFICITY: Expressed in roots. {ECO:0000269|PubMed:18025467}.
CC -!- INDUCTION: Up-regulated during the early stage of iron deficiency (at
CC protein level). {ECO:0000269|PubMed:27137867}.
CC -!- PTM: Polyubiquitinated (PubMed:27137867). Ubiquitination leads to its
CC subsequent degradation via the proteasome pathway (PubMed:27137867).
CC {ECO:0000269|PubMed:27137867}.
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; AP005406; BAD03551.1; -; Genomic_DNA.
DR EMBL; AP008214; BAF22671.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT03400.1; -; Genomic_DNA.
DR EMBL; CM000145; EEE67890.1; -; Genomic_DNA.
DR EMBL; AK107456; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BR000654; FAA00380.1; -; mRNA.
DR RefSeq; XP_015648159.1; XM_015792673.1.
DR AlphaFoldDB; Q6Z1Z3; -.
DR SMR; Q6Z1Z3; -.
DR STRING; 4530.OS08T0101000-01; -.
DR PaxDb; Q6Z1Z3; -.
DR PRIDE; Q6Z1Z3; -.
DR EnsemblPlants; Os08t0101000-01; Os08t0101000-01; Os08g0101000.
DR GeneID; 4344415; -.
DR Gramene; Os08t0101000-01; Os08t0101000-01; Os08g0101000.
DR KEGG; osa:4344415; -.
DR eggNOG; ENOG502S3BX; Eukaryota.
DR HOGENOM; CLU_025764_1_0_1; -.
DR InParanoid; Q6Z1Z3; -.
DR OMA; MYILDSA; -.
DR OrthoDB; 317013at2759; -.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR Genevisible; Q6Z1Z3; OS.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:UniProtKB.
DR CDD; cd10017; B3_DNA; 1.
DR Gene3D; 2.40.330.10; -; 1.
DR InterPro; IPR003340; B3_DNA-bd.
DR InterPro; IPR015300; DNA-bd_pseudobarrel_sf.
DR InterPro; IPR044800; LEC2-like.
DR PANTHER; PTHR31140; PTHR31140; 1.
DR Pfam; PF02362; B3; 1.
DR SMART; SM01019; B3; 1.
DR SUPFAM; SSF101936; SSF101936; 1.
DR PROSITE; PS50863; B3; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation; Ubl conjugation.
FT CHAIN 1..362
FT /note="B3 domain-containing protein IDEF1"
FT /id="PRO_0000376938"
FT DNA_BIND 253..355
FT /note="TF-B3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00326"
FT REGION 30..91
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 52..66
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 229
FT /note="L -> F (in Ref. 5; AK107456)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 362 AA; 39942 MW; 70F577BAEEB4763D CRC64;
MGQMDGGDGG GGGHPYHYQA LLAAVHQQTV PFPNPFPAPS SGAEPPHPHN HNHNHNHNHN
IHNSHNHNHN HNAAPHPCHT PTPTPTPRGF ADWSASTSAF TSLAAHSSTA PSNAVHYSFS
PCYAFWTHYM LNKNAYPTSF PAPHDDHLRL ANNNHPRDAP GPASSYGVES FTSPSMAPNI
CTHMPPIEGP ISAKEDKKPE ILPRVVKSSD ELETRNSNVE FHSETVGTLP ESKQGHDSRA
TKLLNSGEYQ VILRKELTKS DVGNVGRIVL PKKDAEASLP PLLQRDPLIL HMDDMVLPVT
WKFKYRYWPN NKSRMYILDS AGEFLKTHGL QAGDVIIIYK NLAPGKFIIR GEKAIHQQTT
NP
