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Single-stranded DNA-binding protein WHY3, chloroplastic (Protein PLASTID TRANSCRIPTIONALLY ACTIVE 11) (Protein WHIRLY 3) (AtWHY3)

 WHY3_ARATH              Reviewed;         268 AA.
Q66GR6; A8MR64; O64508; Q0WLJ4;
28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
11-OCT-2004, sequence version 1.
23-MAY-2018, entry version 98.
RecName: Full=Single-stranded DNA-binding protein WHY3, chloroplastic;
AltName: Full=Protein PLASTID TRANSCRIPTIONALLY ACTIVE 11;
AltName: Full=Protein WHIRLY 3;
Short=AtWHY3;
Flags: Precursor;
Name=WHY3; Synonyms=PTAC11; OrderedLocusNames=At2g02740;
ORFNames=T20F6.12;
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 [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[2]
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).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=cv. Columbia;
Kim C.J., Chen H., Cheuk R.F., Shinn P., Ecker J.R.;
"Arabidopsis ORF clones.";
Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
[5]
SUBCELLULAR LOCATION, GENE FAMILY, AND NOMENCLATURE.
PubMed=15967440; DOI=10.1016/j.febslet.2005.05.059;
Krause K., Kilbienski I., Mulisch M., Roediger A., Schaefer A.,
Krupinska K.;
"DNA-binding proteins of the Whirly family in Arabidopsis thaliana are
targeted to the organelles.";
FEBS Lett. 579:3707-3712(2005).
[6]
GENE FAMILY.
PubMed=15708347; DOI=10.1016/j.tplants.2004.12.008;
Desveaux D., Marechal A., Brisson N.;
"Whirly transcription factors: defense gene regulation and beyond.";
Trends Plant Sci. 10:95-102(2005).
[7]
FUNCTION, INDUCTION BY SALICYLIC ACID, AND IDENTIFICATION BY MASS
SPECTROMETRY.
PubMed=19669906; DOI=10.1007/s11103-009-9533-7;
Xiong J.Y., Lai C.X., Qu Z., Yang X.Y., Qin X.H., Liu G.Q.;
"Recruitment of AtWHY1 and AtWHY3 by a distal element upstream of the
kinesin gene AtKP1 to mediate transcriptional repression.";
Plant Mol. Biol. 71:437-449(2009).
[8]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=19666500; DOI=10.1073/pnas.0901710106;
Marechal A., Parent J.S., Veronneau-Lafortune F., Joyeux A.,
Lang B.F., Brisson N.;
"Whirly proteins maintain plastid genome stability in Arabidopsis.";
Proc. Natl. Acad. Sci. U.S.A. 106:14693-14698(2009).
[9]
FUNCTION.
PubMed=20551348; DOI=10.1105/tpc.109.071399;
Cappadocia L., Marechal A., Parent J.S., Lepage E., Sygusch J.,
Brisson N.;
"Crystal structures of DNA-Whirly complexes and their role in
Arabidopsis organelle genome repair.";
Plant Cell 22:1849-1867(2010).
[10]
FUNCTION, AND MUTAGENESIS OF LYS-95.
PubMed=21911368; DOI=10.1093/nar/gkr740;
Cappadocia L., Parent J.S., Zampini E., Lepage E., Sygusch J.,
Brisson N.;
"A conserved lysine residue of plant Whirly proteins is necessary for
higher order protein assembly and protection against DNA damage.";
Nucleic Acids Res. 40:258-269(2012).
-!- FUNCTION: Single-stranded DNA-binding protein that functions in
both chloroplasts and nucleus. In chloroplasts, maintains plastid
genome stability by preventing break-induced and short homology-
dependent illegitimate recombinations. In the nucleus, is
recruited to a distal element upstream of the kinesin KP1 to
mediate the transcriptional repression of KP1. Can bind double-
stranded DNA in vivo. {ECO:0000269|PubMed:19666500,
ECO:0000269|PubMed:19669906, ECO:0000269|PubMed:20551348,
ECO:0000269|PubMed:21911368}.
-!- SUBUNIT: Homotetramer. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast
{ECO:0000269|PubMed:15967440}. Nucleus {ECO:0000250}. Note=Can
localize to both chloroplast and nucleus. {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q66GR6-1; Sequence=Displayed;
Name=2;
IsoId=Q66GR6-2; Sequence=VSP_044508;
Note=Derived from EST data. May be due to a competing acceptor
splice site. No experimental confirmation available.;
-!- INDUCTION: By salicylic acid (SA). {ECO:0000269|PubMed:19669906}.
-!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
conditions. {ECO:0000269|PubMed:19666500}.
-!- SIMILARITY: Belongs to the Whirly family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAC05348.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AC002521; AAC05348.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002685; AEC05618.1; -; Genomic_DNA.
EMBL; BT015336; AAU05459.1; -; mRNA.
EMBL; BT015641; AAU15140.1; -; mRNA.
EMBL; AK230205; BAF02013.1; -; mRNA.
PIR; T00854; T00854.
RefSeq; NP_178377.2; NM_126329.4. [Q66GR6-1]
UniGene; At.41460; -.
UniGene; At.66386; -.
PDB; 4KOQ; X-ray; 1.85 A; A=78-246.
PDBsum; 4KOQ; -.
ProteinModelPortal; Q66GR6; -.
SMR; Q66GR6; -.
IntAct; Q66GR6; 3.
STRING; 3702.AT2G02740.1; -.
PaxDb; Q66GR6; -.
PRIDE; Q66GR6; -.
EnsemblPlants; AT2G02740.1; AT2G02740.1; AT2G02740. [Q66GR6-1]
GeneID; 814803; -.
Gramene; AT2G02740.1; AT2G02740.1; AT2G02740. [Q66GR6-1]
KEGG; ath:AT2G02740; -.
Araport; AT2G02740; -.
TAIR; locus:2058822; AT2G02740.
eggNOG; ENOG410IFH8; Eukaryota.
eggNOG; ENOG41124UZ; LUCA.
HOGENOM; HOG000006196; -.
InParanoid; Q66GR6; -.
OMA; EPKAPEF; -.
OrthoDB; EOG09360IVL; -.
PhylomeDB; Q66GR6; -.
PRO; PR:Q66GR6; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; Q66GR6; baseline and differential.
Genevisible; Q66GR6; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
GO; GO:0009295; C:nucleoid; IDA:TAIR.
GO; GO:0009508; C:plastid chromosome; IDA:TAIR.
GO; GO:0003677; F:DNA binding; IDA:TAIR.
GO; GO:0003729; F:mRNA binding; IDA:TAIR.
GO; GO:0003697; F:single-stranded DNA binding; IEA:InterPro.
GO; GO:0006952; P:defense response; TAS:TAIR.
GO; GO:0006281; P:DNA repair; IMP:TAIR.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 2.30.31.10; -; 1.
InterPro; IPR009044; ssDNA-bd_transcriptional_reg.
InterPro; IPR013742; Whirly.
PANTHER; PTHR31745; PTHR31745; 1.
Pfam; PF08536; Whirly; 1.
SUPFAM; SSF54447; SSF54447; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chloroplast; Complete proteome;
DNA damage; DNA repair; DNA-binding; Nucleus; Plastid;
Reference proteome; Transcription; Transcription regulation;
Transit peptide.
TRANSIT 1 75 Chloroplast. {ECO:0000255}.
CHAIN 76 268 Single-stranded DNA-binding protein WHY3,
chloroplastic.
/FTId=PRO_0000420449.
REGION 93 98 Required for ssDNA binding.
{ECO:0000250}.
MOTIF 171 185 Nuclear localization signal.
{ECO:0000255}.
VAR_SEQ 175 175 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_044508.
MUTAGEN 95 95 K->A: No effect on DNA binding. Affects
its function in DNA repair.
{ECO:0000269|PubMed:21911368}.
CONFLICT 40 40 A -> T (in Ref. 4; BAF02013).
{ECO:0000305}.
CONFLICT 140 142 RKQ -> KKR (in Ref. 4; BAF02013).
{ECO:0000305}.
STRAND 89 92 {ECO:0000244|PDB:4KOQ}.
STRAND 94 103 {ECO:0000244|PDB:4KOQ}.
STRAND 106 109 {ECO:0000244|PDB:4KOQ}.
STRAND 115 119 {ECO:0000244|PDB:4KOQ}.
STRAND 122 132 {ECO:0000244|PDB:4KOQ}.
HELIX 138 140 {ECO:0000244|PDB:4KOQ}.
STRAND 142 146 {ECO:0000244|PDB:4KOQ}.
HELIX 148 155 {ECO:0000244|PDB:4KOQ}.
STRAND 163 167 {ECO:0000244|PDB:4KOQ}.
STRAND 171 173 {ECO:0000244|PDB:4KOQ}.
TURN 176 178 {ECO:0000244|PDB:4KOQ}.
STRAND 179 188 {ECO:0000244|PDB:4KOQ}.
STRAND 192 203 {ECO:0000244|PDB:4KOQ}.
TURN 204 207 {ECO:0000244|PDB:4KOQ}.
STRAND 208 217 {ECO:0000244|PDB:4KOQ}.
HELIX 218 235 {ECO:0000244|PDB:4KOQ}.
HELIX 238 242 {ECO:0000244|PDB:4KOQ}.
SEQUENCE 268 AA; 29728 MW; 8E27F7A0512991D7 CRC64;
MSQLLSSPPM AVFSKTFINH KFSDARFLSS HSILTSGGFA GKIIPLKPTA RLKLTVKSRQ
SDYFEKQRFG DSSSSQNAEV SSPRFYVGHS IYKGKAALTI EPRAPEFVAL ESGAFKLTKE
GFLLLQFAPA AGVRQYDWSR KQVFSLSVTE IGNLVSLGPR ESCEFFHDPF KGKGSDEGKV
RKVLKVEPLP DGSGRFFNLS VQNKLLNVDE SVYIPITKAE FAVLISAFNF VLPHLIGWSA
FANSIKPEDS NRLNNASPKY GGDYEWSR


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