PKL_ARATH
ID PKL_ARATH Reviewed; 1384 AA.
AC Q9S775; Q0WNM8;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=CHD3-type chromatin-remodeling factor PICKLE;
DE EC=3.6.4.-;
DE AltName: Full=Protein CHROMATIN REMODELING 6 {ECO:0000303|PubMed:16547115};
DE Short=AtCHR6;
DE AltName: Full=Protein GYMNOS;
GN Name=PKL; Synonyms=CHR6 {ECO:0000303|PubMed:16547115}, GYM;
GN OrderedLocusNames=At2g25170; ORFNames=F13D4.130;
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 [MRNA], FUNCTION, TISSUE SPECIFICITY, AND MUTAGENESIS
RP OF GLY-451.
RC STRAIN=cv. Columbia;
RX PubMed=10535738; DOI=10.1016/s0092-8674(00)81651-7;
RA Eshed Y., Baum S.F., Bowman J.L.;
RT "Distinct mechanisms promote polarity establishment in carpels of
RT Arabidopsis.";
RL Cell 99:199-209(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10570159; DOI=10.1073/pnas.96.24.13839;
RA Ogas J., Kaufmann S., Henderson J., Somerville C.;
RT "PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition
RT from embryonic to vegetative development in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:13839-13844(1999).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 419-1384.
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 [6]
RP FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP 633-HIS--LYS-635.
RX PubMed=16359393; DOI=10.1111/j.1365-313x.2005.02602.x;
RA Li H.-C., Chuang K., Henderson J.T., Rider S.D. Jr., Bai Y., Zhang H.,
RA Fountain M., Gerber J., Ogas J.;
RT "PICKLE acts during germination to repress expression of embryonic
RT traits.";
RL Plant J. 44:1010-1022(2005).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16547115; DOI=10.1534/genetics.105.051664;
RA Shaked H., Avivi-Ragolsky N., Levy A.A.;
RT "Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family
RT in DNA damage response and recombination.";
RL Genetics 173:985-994(2006).
RN [8]
RP SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [10]
RP FUNCTION, MUTAGENESIS OF GLY-301, INTERACTION WITH TAF12B, DISRUPTION
RP PHENOTYPE, AND INDUCTION BY CYTOKININS.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=21357580; DOI=10.1093/pcp/pcr022;
RA Furuta K., Kubo M., Sano K., Demura T., Fukuda H., Liu Y.G., Shibata D.,
RA Kakimoto T.;
RT "The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin
RT responses in Arabidopsis calli.";
RL Plant Cell Physiol. 52:618-628(2011).
RN [11]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
CC -!- FUNCTION: Chromatin remodeling factor that represses the expression of
CC embryonic trait genes (such as NFYB9/LEC1) upon and after seed
CC germination and thus enables the developmental switch to post-
CC germinative growth. Silences some MADS-box proteins such as PHE1 and
CC PHE2. Plays a role during carpel differentiation. Regulates late
CC processes in cytokinin signaling. {ECO:0000269|PubMed:10535738,
CC ECO:0000269|PubMed:10570159, ECO:0000269|PubMed:16359393,
CC ECO:0000269|PubMed:21357580}.
CC -!- SUBUNIT: Interacts with TAF12B. {ECO:0000269|PubMed:21357580}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:16359393, ECO:0000269|PubMed:19245862}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in tissue undergoing significant
CC differentiation (meristems and primordia) such as young seedlings,
CC influorescent tissue and young siliques, but not in endosperm and seed
CC coat (at protein level). Levels decrease as organs age. Also present in
CC trichomes. {ECO:0000269|PubMed:10535738, ECO:0000269|PubMed:10570159,
CC ECO:0000269|PubMed:16359393}.
CC -!- INDUCTION: Not up-regulated by cytokinins.
CC {ECO:0000269|PubMed:21357580}.
CC -!- DISRUPTION PHENOTYPE: Hypersensitivity to cytokinins.
CC {ECO:0000269|PubMed:21357580}.
CC -!- MISCELLANEOUS: 'Gymnos' means 'naked' in Greek.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
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DR EMBL; AF185578; AAF07084.1; -; mRNA.
DR EMBL; AF185577; AAF13875.1; -; mRNA.
DR EMBL; CP002685; AEC07666.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM62112.1; -; Genomic_DNA.
DR EMBL; AK229409; BAF01271.1; -; mRNA.
DR PIR; T52301; T52301.
DR RefSeq; NP_001324291.1; NM_001335978.1.
DR RefSeq; NP_565587.1; NM_128074.4.
DR AlphaFoldDB; Q9S775; -.
DR SMR; Q9S775; -.
DR BioGRID; 2407; 35.
DR STRING; 3702.AT2G25170.1; -.
DR iPTMnet; Q9S775; -.
DR PaxDb; Q9S775; -.
DR PRIDE; Q9S775; -.
DR ProteomicsDB; 235032; -.
DR EnsemblPlants; AT2G25170.1; AT2G25170.1; AT2G25170.
DR EnsemblPlants; AT2G25170.4; AT2G25170.4; AT2G25170.
DR GeneID; 817055; -.
DR Gramene; AT2G25170.1; AT2G25170.1; AT2G25170.
DR Gramene; AT2G25170.4; AT2G25170.4; AT2G25170.
DR KEGG; ath:AT2G25170; -.
DR Araport; AT2G25170; -.
DR TAIR; locus:2040184; AT2G25170.
DR eggNOG; KOG0383; Eukaryota.
DR HOGENOM; CLU_000315_31_0_1; -.
DR InParanoid; Q9S775; -.
DR OMA; MINMDST; -.
DR PhylomeDB; Q9S775; -.
DR PRO; PR:Q9S775; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9S775; baseline and differential.
DR Genevisible; Q9S775; AT.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IBA:GO_Central.
DR GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IBA:GO_Central.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; ISS:TAIR.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IMP:TAIR.
DR GO; GO:0009992; P:cellular water homeostasis; IMP:TAIR.
DR GO; GO:0006338; P:chromatin remodeling; ISS:TAIR.
DR GO; GO:0009736; P:cytokinin-activated signaling pathway; IMP:TAIR.
DR GO; GO:0009788; P:negative regulation of abscisic acid-activated signaling pathway; IMP:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IMP:TAIR.
DR GO; GO:2000023; P:regulation of lateral root development; IMP:TAIR.
DR GO; GO:0009733; P:response to auxin; IMP:TAIR.
DR GO; GO:0009739; P:response to gibberellin; IMP:TAIR.
DR GO; GO:0009414; P:response to water deprivation; IMP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.40.50.10810; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR009462; CHD_II_SANT-like.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR InterPro; IPR023780; Chromo_domain.
DR InterPro; IPR009463; DUF1087.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR038718; SNF2-like_sf.
DR InterPro; IPR000330; SNF2_N.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00385; Chromo; 2.
DR Pfam; PF06461; DUF1086; 1.
DR Pfam; PF06465; DUF1087; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF00176; SNF2-rel_dom; 1.
DR SMART; SM00298; CHROMO; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM01146; DUF1086; 1.
DR SMART; SM01147; DUF1087; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF54160; SSF54160; 2.
DR PROSITE; PS50013; CHROMO_2; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Chromatin regulator; DNA-binding; Helicase; Hydrolase;
KW Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Zinc; Zinc-finger.
FT CHAIN 1..1384
FT /note="CHD3-type chromatin-remodeling factor PICKLE"
FT /id="PRO_0000233174"
FT DOMAIN 98..180
FT /note="Chromo 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 190..249
FT /note="Chromo 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 285..471
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 599..760
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 49..96
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 893..941
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1122..1152
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1313..1344
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1365..1384
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 376..383
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 422..425
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 893..910
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1315..1341
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1366..1384
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 298..305
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 23
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT MUTAGEN 301
FT /note="G->R: In chk2-2; hypersensitivity to cytokinins."
FT /evidence="ECO:0000269|PubMed:21357580"
FT MUTAGEN 451
FT /note="G->E: In gym-4; when associated with a lack of CRC,
FT morphological aberrations including shorter and narrower
FT carpels containing external ovules."
FT /evidence="ECO:0000269|PubMed:10535738"
FT MUTAGEN 633..635
FT /note="Missing: In pkl-1; embryonic traits expressed after
FT germination including pickle roots (primary roots of adult
FT plants that express embryonic differentiation traits such
FT as expression of storage protein genes and accumulation of
FT storage lipids)."
FT /evidence="ECO:0000269|PubMed:16359393"
FT CONFLICT 419
FT /note="M -> L (in Ref. 5; BAF01271)"
FT /evidence="ECO:0000305"
FT CONFLICT 565
FT /note="K -> R (in Ref. 5; BAF01271)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1384 AA; 158405 MW; C4EDC75D7D973264 CRC64;
MSSLVERLRI RSDRKPVYNL DDSDDDDFVP KKDRTFEQVE AIVRTDAKEN ACQACGESTN
LVSCNTCTYA FHAKCLVPPL KDASVENWRC PECVSPLNEI DKILDCEMRP TKSSEQGSSD
AEPKPIFVKQ YLVKWKGLSY LHCSWVPEKE FQKAYKSNHR LKTRVNNFHR QMESFNNSED
DFVAIRPEWT TVDRILACRE EDGELEYLVK YKELSYDECY WESESDISTF QNEIQRFKDV
NSRTRRSKDV DHKRNPRDFQ QFDHTPEFLK GLLHPYQLEG LNFLRFSWSK QTHVILADEM
GLGKTIQSIA LLASLFEENL IPHLVIAPLS TLRNWEREFA TWAPQMNVVM YFGTAQARAV
IREHEFYLSK DQKKIKKKKS GQISSESKQK RIKFDVLLTS YEMINLDSAV LKPIKWECMI
VDEGHRLKNK DSKLFSSLTQ YSSNHRILLT GTPLQNNLDE LFMLMHFLDA GKFGSLEEFQ
EEFKDINQEE QISRLHKMLA PHLLRRVKKD VMKDMPPKKE LILRVDLSSL QKEYYKAIFT
RNYQVLTKKG GAQISLNNIM MELRKVCCHP YMLEGVEPVI HDANEAFKQL LESCGKLQLL
DKMMVKLKEQ GHRVLIYTQF QHMLDLLEDY CTHKKWQYER IDGKVGGAER QIRIDRFNAK
NSNKFCFLLS TRAGGLGINL ATADTVIIYD SDWNPHADLQ AMARAHRLGQ TNKVMIYRLI
NRGTIEERMM QLTKKKMVLE HLVVGKLKTQ NINQEELDDI IRYGSKELFA SEDDEAGKSG
KIHYDDAAID KLLDRDLVEA EEVSVDDEEE NGFLKAFKVA NFEYIDENEA AALEAQRVAA
ESKSSAGNSD RASYWEELLK DKFELHQAEE LNALGKRKRS RKQLVSIEED DLAGLEDVSS
DGDESYEAES TDGEAAGQGV QTGRRPYRRK GRDNLEPTPL MEGEGRSFRV LGFNQSQRAI
FVQTLMRYGA GNFDWKEFVP RLKQKTFEEI NEYGILFLKH IAEEIDENSP TFSDGVPKEG
LRIEDVLVRI ALLILVQEKV KFVEDHPGKP VFPSRILERF PGLRSGKIWK EEHDKIMIRA
VLKHGYGRWQ AIVDDKELGI QELICKELNF PHISLSAAEQ AGLQGQNGSG GSNPGAQTNQ
NPGSVITGNN NASADGAQVN SMFYYRDMQR RLVEFVKKRV LLLEKAMNYE YAEEYYGLGG
SSSIPTEEPE AEPKIADTVG VSFIEVDDEM LDGLPKTDPI TSEEIMGAAV DNNQARVEIA
QHYNQMCKLL DENARESVQA YVNNQPPSTK VNESFRALKS INGNINTILS ITSDQSKSHE
DDTKPDLNNV EMKDTAEETK PLRGGVVDLN VVEGEENIAE ASGSVDVKME EAKEEEKPKN
MVVD
