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Squamosa promoter-binding-like protein 7

 SPL7_ARATH              Reviewed;         801 AA.
Q8S9G8; Q8VZV0; Q9S723; Q9SMY1;
07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
07-JUN-2005, sequence version 2.
23-MAY-2018, entry version 107.
RecName: Full=Squamosa promoter-binding-like protein 7;
Name=SPL7; OrderedLocusNames=At5g18830; ORFNames=F17K4.80;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1), AND
DEVELOPMENTAL STAGE.
STRAIN=cv. Columbia, and cv. Landsberg erecta; TISSUE=Flower;
PubMed=10524240; DOI=10.1016/S0378-1119(99)00308-X;
Cardon G.H., Hoehmann S., Klein J., Nettesheim K., Saedler H.,
Huijser P.;
"Molecular characterization of the Arabidopsis SBP-box genes.";
Gene 237:91-104(1999).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130714; DOI=10.1038/35048507;
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K.,
Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S.,
Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
"Sequence and analysis of chromosome 5 of the plant Arabidopsis
thaliana.";
Nature 408:823-826(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
FUNCTION.
PubMed=19122104; DOI=10.1105/tpc.108.060137;
Yamasaki H., Hayashi M., Fukazawa M., Kobayashi Y., Shikanai T.;
"SQUAMOSA promoter binding protein-like7 is a central regulator for
copper homeostasis in Arabidopsis.";
Plant Cell 21:347-361(2009).
[6]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=22374396; DOI=10.1105/tpc.111.090431;
Bernal M., Casero D., Singh V., Wilson G.T., Grande A., Yang H.,
Dodani S.C., Pellegrini M., Huijser P., Connolly E.L., Merchant S.S.,
Kraemer U.;
"Transcriptome sequencing identifies SPL7-regulated copper acquisition
genes FRO4/FRO5 and the copper dependence of iron homeostasis in
Arabidopsis.";
Plant Cell 24:738-761(2012).
[7]
SUBUNIT.
PubMed=25207797; DOI=10.1186/s12870-014-0231-5;
Garcia-Molina A., Xing S., Huijser P.;
"Functional characterisation of Arabidopsis SPL7 conserved protein
domains suggests novel regulatory mechanisms in the Cu deficiency
response.";
BMC Plant Biol. 14:231-231(2014).
[8]
FUNCTION, AND INTERACTION WITH HY5.
PubMed=25516599; DOI=10.1105/tpc.114.127340;
Zhang H., Zhao X., Li J., Cai H., Deng X.W., Li L.;
"MicroRNA408 is critical for the HY5-SPL7 gene network that mediates
the coordinated response to light and copper.";
Plant Cell 26:4933-4953(2014).
[9]
INTERACTION WITH KIN17, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
PubMed=24335506; DOI=10.1104/pp.113.228239;
Garcia-Molina A., Xing S., Huijser P.;
"A conserved KIN17 curved DNA-binding domain protein assembles with
SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 to adapt Arabidopsis growth
and development to limiting copper availability.";
Plant Physiol. 164:828-840(2014).
[10]
FUNCTION.
PubMed=26511915; DOI=10.1104/pp.15.01011;
Zhao Y., Lin S., Qiu Z., Cao D., Wen J., Deng X., Wang X., Lin J.,
Li X.;
"MicroRNA857 is involved in the regulation of secondary growth of
vascular tissues in Arabidopsis.";
Plant Physiol. 169:2539-2552(2015).
[11]
FUNCTION.
PubMed=27352843; DOI=10.1186/s12870-016-0830-4;
Gielen H., Remans T., Vangronsveld J., Cuypers A.;
"Toxicity responses of Cu and Cd: the involvement of miRNAs and the
transcription factor SPL7.";
BMC Plant Biol. 16:145-145(2016).
[12]
STRUCTURE BY NMR OF 135-220, AND ZINC-BINDING SITES CYS-138; CYS-143;
CYS-160; CYS-163; CYS-179; CYS-182; HIS-186 AND CYS-198.
PubMed=15001351; DOI=10.1016/j.jmb.2004.01.015;
Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T.,
Aoki M., Seki E., Matsuda T., Nunokawa E., Ishizuka Y., Terada T.,
Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S.;
"A novel zinc-binding motif revealed by solution structures of DNA-
binding domains of Arabidopsis SBP-family transcription factors.";
J. Mol. Biol. 337:49-63(2004).
-!- FUNCTION: Transcription factor that participates in reprogramming
global gene expression during copper deficiency in order to
improve the metal uptake and prioritize its distribution to copper
proteins of major importance (Probable). Binds directly to 5'-
GTAC-3' motifs in the microRNA (miRNA) promoter of the stress-
responsive miRNAs miR398b and miR398c to activate their
transcription. During copper deficiency, activates the copper
transporters COPT1 and COPT2, and the copper chaperone CCH,
directly or indirectly via miRNAs. Required for the expression of
the miRNAs miR397, miR408 and miR857 (PubMed:19122104). Acts
coordinately with HY5 to regulate miR408 and its target genes in
response to changes in light and copper conditions
(PubMed:25516599). Activates miR857 and its target genes in
response to low copper conditions (PubMed:26511915). Involved in
cadmium stress response by regulating miR397a, miR398b, miR398c
and miR857 (PubMed:27352843). Required for iron homeostasis during
copper deficiency (PubMed:22374396). {ECO:0000269|PubMed:19122104,
ECO:0000269|PubMed:22374396, ECO:0000269|PubMed:25516599,
ECO:0000269|PubMed:26511915, ECO:0000269|PubMed:27352843}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:15001351};
Note=Binds 2 Zn(2+) ions per subunit.
{ECO:0000269|PubMed:15001351};
-!- SUBUNIT: Homodimer (PubMed:25207797). Interacts with KIN17
(PubMed:24335506). Interacts with HY5 (PubMed:25516599).
{ECO:0000269|PubMed:24335506, ECO:0000269|PubMed:25207797,
ECO:0000269|PubMed:25516599}.
-!- SUBCELLULAR LOCATION: Nucleus speckle
{ECO:0000269|PubMed:24335506}. Note=Nuclear localization with a
speckled distribution pattern. {ECO:0000269|PubMed:24335506}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8S9G8-1; Sequence=Displayed;
Name=2;
IsoId=Q8S9G8-2; Sequence=VSP_013984;
Note=No experimental confirmation available. May be due to a
competing donor splice site.;
-!- TISSUE SPECIFICITY: Expressed in roots rosette leaves, cauline
leaves, stems, flowers and siliques.
{ECO:0000269|PubMed:24335506}.
-!- DEVELOPMENTAL STAGE: Expressed constitutively during plant
development. {ECO:0000269|PubMed:10524240}.
-!- DOMAIN: The SBP-type zinc finger is required for the binding to
DNA. {ECO:0000305}.
-!- DISRUPTION PHENOTYPE: Retarded growth and hypersensitivity to
copper deprivation. {ECO:0000269|PubMed:24335506}.
-!- SEQUENCE CAUTION:
Sequence=AAL77751.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AJ011611; CAB56573.1; -; mRNA.
EMBL; AJ011612; CAB56574.1; -; mRNA.
EMBL; AJ011613; CAB56575.1; -; Genomic_DNA.
EMBL; AC068655; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CP002688; AED92617.1; -; Genomic_DNA.
EMBL; CP002688; AED92618.1; -; Genomic_DNA.
EMBL; AF367355; AAK32941.1; -; mRNA.
EMBL; AY063815; AAL36171.1; -; mRNA.
EMBL; AY078050; AAL77751.1; ALT_INIT; mRNA.
PIR; T52605; T52605.
PIR; T52606; T52606.
RefSeq; NP_197384.1; NM_121888.3. [Q8S9G8-1]
RefSeq; NP_850850.1; NM_180519.1. [Q8S9G8-2]
UniGene; At.495; -.
PDB; 1UL5; NMR; -; A=135-220.
PDBsum; 1UL5; -.
ProteinModelPortal; Q8S9G8; -.
SMR; Q8S9G8; -.
BioGrid; 17277; 2.
IntAct; Q8S9G8; 1.
STRING; 3702.AT5G18830.3; -.
PaxDb; Q8S9G8; -.
PRIDE; Q8S9G8; -.
EnsemblPlants; AT5G18830.1; AT5G18830.1; AT5G18830. [Q8S9G8-1]
EnsemblPlants; AT5G18830.2; AT5G18830.2; AT5G18830. [Q8S9G8-2]
GeneID; 832001; -.
Gramene; AT5G18830.1; AT5G18830.1; AT5G18830. [Q8S9G8-1]
Gramene; AT5G18830.2; AT5G18830.2; AT5G18830. [Q8S9G8-2]
KEGG; ath:AT5G18830; -.
Araport; AT5G18830; -.
eggNOG; ENOG410IF57; Eukaryota.
eggNOG; ENOG4111YFE; LUCA.
HOGENOM; HOG000084016; -.
InParanoid; Q8S9G8; -.
PhylomeDB; Q8S9G8; -.
EvolutionaryTrace; Q8S9G8; -.
PRO; PR:Q8S9G8; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q8S9G8; baseline and differential.
Genevisible; Q8S9G8; AT.
GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0035874; P:cellular response to copper ion starvation; IMP:UniProtKB.
GO; GO:0048638; P:regulation of developmental growth; IMP:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:UniProtKB.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 4.10.1100.10; -; 1.
InterPro; IPR004333; SBP_dom.
InterPro; IPR036893; SBP_sf.
Pfam; PF03110; SBP; 1.
SUPFAM; SSF103612; SSF103612; 1.
PROSITE; PS51141; ZF_SBP; 1.
1: Evidence at protein level;
3D-structure; Activator; Alternative splicing; Complete proteome;
DNA-binding; Metal-binding; Nucleus; Reference proteome;
Stress response; Transcription; Transcription regulation; Zinc;
Zinc-finger.
CHAIN 1 801 Squamosa promoter-binding-like protein 7.
/FTId=PRO_0000132728.
ZN_FING 135 212 SBP-type. {ECO:0000255|PROSITE-
ProRule:PRU00470}.
MOTIF 195 211 Bipartite nuclear localization signal.
{ECO:0000255}.
COMPBIAS 8 18 Pro-rich.
COMPBIAS 55 80 Pro-rich.
METAL 138 138 Zinc 1. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 143 143 Zinc 1. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 160 160 Zinc 1. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 163 163 Zinc 1. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 182 182 Zinc 2. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 186 186 Zinc 2; via tele nitrogen.
{ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
METAL 198 198 Zinc 2. {ECO:0000244|PDB:1UL5,
ECO:0000269|PubMed:15001351}.
VAR_SEQ 675 700 Missing (in isoform 2).
{ECO:0000303|PubMed:14593172}.
/FTId=VSP_013984.
CONFLICT 165 165 T -> N (in Ref. 1; CAB56573).
{ECO:0000305}.
STRAND 152 154 {ECO:0000244|PDB:1UL5}.
HELIX 155 157 {ECO:0000244|PDB:1UL5}.
HELIX 161 166 {ECO:0000244|PDB:1UL5}.
STRAND 167 171 {ECO:0000244|PDB:1UL5}.
STRAND 174 178 {ECO:0000244|PDB:1UL5}.
TURN 180 182 {ECO:0000244|PDB:1UL5}.
STRAND 183 187 {ECO:0000244|PDB:1UL5}.
HELIX 188 190 {ECO:0000244|PDB:1UL5}.
STRAND 197 201 {ECO:0000244|PDB:1UL5}.
STRAND 205 207 {ECO:0000244|PDB:1UL5}.
SEQUENCE 801 AA; 89617 MW; E69BE9C57670090D CRC64;
MSSLSQSPPP PEMDIQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLVD QIHFPPVLSP
PLPPLIPTQT PAESELDPSP EESGSGSDRV RKRDPRLICS NFIEGMLPCS CPELDQKLED
AELPKKKRVR GGSGVARCQV PDCEADISEL KGYHKRHRVC LRCATASFVV LDGENKRYCQ
QCGKFHLLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA AEQQQVLSQN DNSVIDVEDG
KDITCSSDQR AEEEPSLIFE DRHITTQGSV PFTRSINADN FVSVTGSGEA QPDEGMNDTK
FERSPSNGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLANM PVELEGYIRP
GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN MIFRLIKGGT
TLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG KYLPHNYSVV
PAPDQDGKRS CNNKFYKINI VNSDPSLFGP AFVEVENESG LSNFIPLIIG DAAVCSEMKL
IEQKFNATLF PEGQEVTACS SLTCCCRDFG ERQSTFSGLL LDIAWSVKVP SAERTEQPVN
RCQIKRYNRV LNYLIQNNSA SILGNVLHNL ETLVKKMEPD SLVHCTCDCD VRLLHENMDL
ASDIHRKHQS PIESKVNPPS SGCCCVSSQK DIPSRILNFN KDPEAGLDCK ERIQADCSPD
SGGKETDPLL NKEVVMNVND IGDWPRKSCI KTHSALAFRS RQTMFLIATF AVCFAVCAVL
YHPNKVTQLA VAIRMRLVHK I


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