SPL4_ARATH
ID SPL4_ARATH Reviewed; 174 AA.
AC Q9S7A9; Q9SMX8;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Squamosa promoter-binding-like protein 4;
GN Name=SPL4; OrderedLocusNames=At1g53160; ORFNames=F12M16.2;
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 [GENOMIC DNA / MRNA], FUNCTION, TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta; TISSUE=Flower;
RX PubMed=10524240; DOI=10.1016/s0378-1119(99)00308-x;
RA Cardon G.H., Hoehmann S., Klein J., Nettesheim K., Saedler H., Huijser P.;
RT "Molecular characterization of the Arabidopsis SBP-box genes.";
RL Gene 237:91-104(1999).
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].
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].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP INDUCTION.
RX PubMed=12202040; DOI=10.1016/s0092-8674(02)00863-2;
RA Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P.;
RT "Prediction of plant microRNA targets.";
RL Cell 110:513-520(2002).
RN [7]
RP DEVELOPMENTAL STAGE.
RX PubMed=14573523; DOI=10.1242/dev.00842;
RA Schmid M., Uhlenhaut N.H., Godard F., Demar M., Bressan R., Weigel D.,
RA Lohmann J.U.;
RT "Dissection of floral induction pathways using global expression
RT analysis.";
RL Development 130:6001-6012(2003).
RN [8]
RP STRUCTURE BY NMR OF 51-132, AND ZINC-BINDING SITES CYS-54; CYS-59; CYS-76;
RP HIS-79; CYS-95; CYS-98; HIS-102 AND CYS-114.
RX PubMed=15001351; DOI=10.1016/j.jmb.2004.01.015;
RA Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T.,
RA Aoki M., Seki E., Matsuda T., Nunokawa E., Ishizuka Y., Terada T.,
RA Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S.;
RT "A novel zinc-binding motif revealed by solution structures of DNA-binding
RT domains of Arabidopsis SBP-family transcription factors.";
RL J. Mol. Biol. 337:49-63(2004).
RN [9]
RP SUBCELLULAR LOCATION.
RX PubMed=16095614; DOI=10.1016/j.jmb.2005.07.013;
RA Birkenbihl R.P., Jach G., Saedler H., Huijser P.;
RT "Functional dissection of the plant-specific SBP-domain: overlap of the
RT DNA-binding and nuclear localization domains.";
RL J. Mol. Biol. 352:585-596(2005).
RN [10]
RP FUNCTION, AND INDUCTION.
RX PubMed=16914499; DOI=10.1242/dev.02521;
RA Wu G., Poethig R.S.;
RT "Temporal regulation of shoot development in Arabidopsis thaliana by miR156
RT and its target SPL3.";
RL Development 133:3539-3547(2006).
CC -!- FUNCTION: Trans-acting factor that binds specifically to the consensus
CC nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Promotes both
CC vegetative phase change and flowering. {ECO:0000269|PubMed:10524240,
CC ECO:0000269|PubMed:16914499}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 2 Zn(2+) ions per subunit.;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16095614}. Cytoplasm
CC {ECO:0000269|PubMed:16095614}. Note=Mostly located in nucleus.
CC -!- TISSUE SPECIFICITY: Expressed in the rib meristem and inter-primordial
CC tissue of the inflorescence apex. {ECO:0000269|PubMed:10524240}.
CC -!- DEVELOPMENTAL STAGE: Increases during floral transition and stay high
CC thereafter. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523}.
CC -!- INDUCTION: Negatively regulated by microRNAs miR156 and miR157.
CC {ECO:0000305|PubMed:12202040, ECO:0000305|PubMed:16914499}.
CC -!- DOMAIN: The SBP-type zinc finger is required for the binding to DNA.
CC {ECO:0000250}.
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DR EMBL; AJ011630; CAB56582.1; -; Genomic_DNA.
DR EMBL; AJ011631; CAB56583.1; -; mRNA.
DR EMBL; AJ011632; CAB56584.1; -; mRNA.
DR EMBL; AC008007; AAF69527.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32896.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32897.1; -; Genomic_DNA.
DR EMBL; BT002856; AAO22673.1; -; mRNA.
DR EMBL; BT004391; AAO42385.1; -; mRNA.
DR EMBL; AY084902; AAM61465.1; -; mRNA.
DR PIR; T52599; T52599.
DR PIR; T52600; T52600.
DR RefSeq; NP_175723.1; NM_104194.4.
DR RefSeq; NP_974014.1; NM_202285.2.
DR PDB; 1UL4; NMR; -; A=51-131.
DR PDBsum; 1UL4; -.
DR AlphaFoldDB; Q9S7A9; -.
DR SMR; Q9S7A9; -.
DR BioGRID; 26974; 5.
DR IntAct; Q9S7A9; 4.
DR STRING; 3702.AT1G53160.2; -.
DR iPTMnet; Q9S7A9; -.
DR PaxDb; Q9S7A9; -.
DR PRIDE; Q9S7A9; -.
DR ProteomicsDB; 228291; -.
DR EnsemblPlants; AT1G53160.1; AT1G53160.1; AT1G53160.
DR EnsemblPlants; AT1G53160.2; AT1G53160.2; AT1G53160.
DR GeneID; 841749; -.
DR Gramene; AT1G53160.1; AT1G53160.1; AT1G53160.
DR Gramene; AT1G53160.2; AT1G53160.2; AT1G53160.
DR KEGG; ath:AT1G53160; -.
DR Araport; AT1G53160; -.
DR TAIR; locus:2009675; AT1G53160.
DR eggNOG; ENOG502RZTN; Eukaryota.
DR HOGENOM; CLU_065896_0_0_1; -.
DR InParanoid; Q9S7A9; -.
DR OMA; STYHADE; -.
DR OrthoDB; 1349088at2759; -.
DR PhylomeDB; Q9S7A9; -.
DR EvolutionaryTrace; Q9S7A9; -.
DR PRO; PR:Q9S7A9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9S7A9; baseline and differential.
DR Genevisible; Q9S7A9; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0009908; P:flower development; IEA:InterPro.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR GO; GO:0010321; P:regulation of vegetative phase change; IMP:TAIR.
DR Gene3D; 4.10.1100.10; -; 1.
DR InterPro; IPR004333; SBP_dom.
DR InterPro; IPR017238; SBP_fam.
DR InterPro; IPR036893; SBP_sf.
DR InterPro; IPR044817; SPL.
DR PANTHER; PTHR31251; PTHR31251; 1.
DR Pfam; PF03110; SBP; 1.
DR PIRSF; PIRSF037575; SBP; 1.
DR SUPFAM; SSF103612; SSF103612; 1.
DR PROSITE; PS51141; ZF_SBP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..174
FT /note="Squamosa promoter-binding-like protein 4"
FT /id="PRO_0000132725"
FT ZN_FING 51..128
FT /note="SBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 118..148
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 155..174
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 111..127
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 1..21
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 54
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 59
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 76
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 114
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT HELIX 68..72
FT /evidence="ECO:0007829|PDB:1UL4"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:1UL4"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:1UL4"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:1UL4"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:1UL4"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:1UL4"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:1UL4"
FT TURN 116..119
FT /evidence="ECO:0007829|PDB:1UL4"
SQ SEQUENCE 174 AA; 20120 MW; B569272D389655AB CRC64;
MEGKRSQGQG YMKKKSYLVE EDMETDTDEE EEVGRDRVRG SRGSINRGGS LRLCQVDRCT
ADMKEAKLYH RRHKVCEVHA KASSVFLSGL NQRFCQQCSR FHDLQEFDEA KRSCRRRLAG
HNERRRKSSG ESTYGEGSGR RGINGQVVMQ NQERSRVEMT LPMPNSSFKR PQIR
