WHY3_ARATH
ID WHY3_ARATH Reviewed; 268 AA.
AC Q66GR6; A8MR64; O64508; Q0WLJ4;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 25-MAY-2022, entry version 113.
DE RecName: Full=Single-stranded DNA-binding protein WHY3, chloroplastic;
DE AltName: Full=Protein PLASTID TRANSCRIPTIONALLY ACTIVE 11;
DE AltName: Full=Protein WHIRLY 3;
DE Short=AtWHY3;
DE Flags: Precursor;
GN Name=WHY3; Synonyms=PTAC11; OrderedLocusNames=At2g02740; ORFNames=T20F6.12;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Cheuk R.F., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SUBCELLULAR LOCATION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=15967440; DOI=10.1016/j.febslet.2005.05.059;
RA Krause K., Kilbienski I., Mulisch M., Roediger A., Schaefer A.,
RA Krupinska K.;
RT "DNA-binding proteins of the Whirly family in Arabidopsis thaliana are
RT targeted to the organelles.";
RL FEBS Lett. 579:3707-3712(2005).
RN [6]
RP GENE FAMILY.
RX PubMed=15708347; DOI=10.1016/j.tplants.2004.12.008;
RA Desveaux D., Marechal A., Brisson N.;
RT "Whirly transcription factors: defense gene regulation and beyond.";
RL Trends Plant Sci. 10:95-102(2005).
RN [7]
RP FUNCTION, INDUCTION BY SALICYLIC ACID, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=19669906; DOI=10.1007/s11103-009-9533-7;
RA Xiong J.Y., Lai C.X., Qu Z., Yang X.Y., Qin X.H., Liu G.Q.;
RT "Recruitment of AtWHY1 and AtWHY3 by a distal element upstream of the
RT kinesin gene AtKP1 to mediate transcriptional repression.";
RL Plant Mol. Biol. 71:437-449(2009).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19666500; DOI=10.1073/pnas.0901710106;
RA Marechal A., Parent J.S., Veronneau-Lafortune F., Joyeux A., Lang B.F.,
RA Brisson N.;
RT "Whirly proteins maintain plastid genome stability in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:14693-14698(2009).
RN [9]
RP FUNCTION.
RX PubMed=20551348; DOI=10.1105/tpc.109.071399;
RA Cappadocia L., Marechal A., Parent J.S., Lepage E., Sygusch J., Brisson N.;
RT "Crystal structures of DNA-Whirly complexes and their role in Arabidopsis
RT organelle genome repair.";
RL Plant Cell 22:1849-1867(2010).
RN [10]
RP FUNCTION, AND MUTAGENESIS OF LYS-95.
RX PubMed=21911368; DOI=10.1093/nar/gkr740;
RA Cappadocia L., Parent J.S., Zampini E., Lepage E., Sygusch J., Brisson N.;
RT "A conserved lysine residue of plant Whirly proteins is necessary for
RT higher order protein assembly and protection against DNA damage.";
RL Nucleic Acids Res. 40:258-269(2012).
CC -!- FUNCTION: Single-stranded DNA-binding protein that functions in both
CC chloroplasts and nucleus. In chloroplasts, maintains plastid genome
CC stability by preventing break-induced and short homology-dependent
CC illegitimate recombinations. In the nucleus, is recruited to a distal
CC element upstream of the kinesin KP1 to mediate the transcriptional
CC repression of KP1. Can bind double-stranded DNA in vivo.
CC {ECO:0000269|PubMed:19666500, ECO:0000269|PubMed:19669906,
CC ECO:0000269|PubMed:20551348, ECO:0000269|PubMed:21911368}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:15967440}. Nucleus {ECO:0000250}. Note=Can localize
CC to both chloroplast and nucleus. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q66GR6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q66GR6-2; Sequence=VSP_044508;
CC -!- INDUCTION: By salicylic acid (SA). {ECO:0000269|PubMed:19669906}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:19666500}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the Whirly family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC05348.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC002521; AAC05348.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC05618.1; -; Genomic_DNA.
DR EMBL; BT015336; AAU05459.1; -; mRNA.
DR EMBL; BT015641; AAU15140.1; -; mRNA.
DR EMBL; AK230205; BAF02013.1; -; mRNA.
DR PIR; T00854; T00854.
DR RefSeq; NP_178377.2; NM_126329.4. [Q66GR6-1]
DR PDB; 4KOQ; X-ray; 1.85 A; A=78-246.
DR PDBsum; 4KOQ; -.
DR AlphaFoldDB; Q66GR6; -.
DR SMR; Q66GR6; -.
DR BioGRID; 205; 4.
DR ComplexPortal; CPX-3586; WHY3 complex.
DR IntAct; Q66GR6; 3.
DR STRING; 3702.AT2G02740.1; -.
DR PaxDb; Q66GR6; -.
DR PRIDE; Q66GR6; -.
DR ProteomicsDB; 242547; -. [Q66GR6-1]
DR EnsemblPlants; AT2G02740.1; AT2G02740.1; AT2G02740. [Q66GR6-1]
DR GeneID; 814803; -.
DR Gramene; AT2G02740.1; AT2G02740.1; AT2G02740. [Q66GR6-1]
DR KEGG; ath:AT2G02740; -.
DR Araport; AT2G02740; -.
DR TAIR; locus:2058822; AT2G02740.
DR eggNOG; ENOG502QRRY; Eukaryota.
DR HOGENOM; CLU_062935_1_0_1; -.
DR InParanoid; Q66GR6; -.
DR OMA; IGWSAFA; -.
DR PhylomeDB; Q66GR6; -.
DR PRO; PR:Q66GR6; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q66GR6; baseline and differential.
DR Genevisible; Q66GR6; AT.
DR GO; GO:0009507; C:chloroplast; IDA:ComplexPortal.
DR GO; GO:0042644; C:chloroplast nucleoid; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:1990391; C:DNA repair complex; IPI:ComplexPortal.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003697; F:single-stranded DNA binding; IEA:InterPro.
DR GO; GO:0006952; P:defense response; TAS:TAIR.
DR GO; GO:0006281; P:DNA repair; IMP:TAIR.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0009863; P:salicylic acid mediated signaling pathway; IDA:ComplexPortal.
DR Gene3D; 2.30.31.10; -; 1.
DR InterPro; IPR009044; ssDNA-bd_transcriptional_reg.
DR InterPro; IPR013742; Whirly.
DR PANTHER; PTHR31745; PTHR31745; 1.
DR Pfam; PF08536; Whirly; 1.
DR SUPFAM; SSF54447; SSF54447; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chloroplast; DNA damage; DNA repair;
KW DNA-binding; Nucleus; Plastid; Reference proteome; Transcription;
KW Transcription regulation; Transit peptide.
FT TRANSIT 1..75
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 76..268
FT /note="Single-stranded DNA-binding protein WHY3,
FT chloroplastic"
FT /id="PRO_0000420449"
FT REGION 93..98
FT /note="Required for ssDNA binding"
FT /evidence="ECO:0000250"
FT MOTIF 171..185
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT VAR_SEQ 175
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044508"
FT MUTAGEN 95
FT /note="K->A: No effect on DNA binding. Affects its function
FT in DNA repair."
FT /evidence="ECO:0000269|PubMed:21911368"
FT CONFLICT 40
FT /note="A -> T (in Ref. 4; BAF02013)"
FT /evidence="ECO:0000305"
FT CONFLICT 140..142
FT /note="RKQ -> KKR (in Ref. 4; BAF02013)"
FT /evidence="ECO:0000305"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 94..103
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 106..109
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 122..132
FT /evidence="ECO:0007829|PDB:4KOQ"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 142..146
FT /evidence="ECO:0007829|PDB:4KOQ"
FT HELIX 148..155
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:4KOQ"
FT TURN 176..178
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 179..188
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 192..203
FT /evidence="ECO:0007829|PDB:4KOQ"
FT TURN 204..207
FT /evidence="ECO:0007829|PDB:4KOQ"
FT STRAND 208..217
FT /evidence="ECO:0007829|PDB:4KOQ"
FT HELIX 218..235
FT /evidence="ECO:0007829|PDB:4KOQ"
FT HELIX 238..242
FT /evidence="ECO:0007829|PDB:4KOQ"
SQ 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
