DEKP3_ARATH
ID DEKP3_ARATH Reviewed; 763 AA.
AC Q9SUA1; B9DFH7; Q0WN52; Q0WSS7; Q0WW14; Q8RWF6;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=DEK domain-containing chromatin-associated protein 3 {ECO:0000303|PubMed:15496452};
DE Short=At-DEK3 {ECO:0000303|PubMed:25387881};
DE Short=AtDEK-3 {ECO:0000303|PubMed:15496452};
DE Short=Protein DEK 3 {ECO:0000303|PubMed:15496452};
GN Name=DEK3 {ECO:0000303|PubMed:15496452, ECO:0000303|PubMed:25387881};
GN OrderedLocusNames=At4g26630 {ECO:0000312|Araport:AT4G26630};
GN ORFNames=T15N24.80 {ECO:0000312|EMBL:CAB43859.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(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] OF 1-407.
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 90-501.
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 240-763.
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 [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, GENE FAMILY, AND
RP NOMENCLATURE.
RX PubMed=15496452; DOI=10.1091/mbc.e04-09-0791;
RA Pendle A.F., Clark G.P., Boon R., Lewandowska D., Lam Y.W., Andersen J.,
RA Mann M., Lamond A.I., Brown J.W., Shaw P.J.;
RT "Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar
RT functions.";
RL Mol. Biol. Cell 16:260-269(2005).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
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 [8]
RP IDENTIFICATION BY 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 [9]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INTERACTION WITH
RP TOP1A; SCC3; AT1G61730; AT1G20940; AT1G13930; DEK4; HDT1; SHL; NIT1;
RP CYP19-1; GEBPL; PDP2; PDP3; HSP70-3; PDS5A; KIN2; RPL11A; HISTONE-H3 AND
RP HISTONE-H4, TISSUE SPECIFICITY, AND REPRESSION BY SALT STRESS.
RC STRAIN=cv. Columbia;
RX PubMed=25387881; DOI=10.1105/tpc.114.129254;
RA Waidmann S., Kusenda B., Mayerhofer J., Mechtler K., Jonak C.;
RT "A DEK domain-containing protein modulates chromatin structure and function
RT in Arabidopsis.";
RL Plant Cell 26:4328-4344(2014).
CC -!- FUNCTION: Chromatin-associated protein which contributes to the
CC modulation of chromatin structure (such as super-helical structure of
CC DNA) and function (PubMed:25387881). Binds to chromatin of protein-
CC coding genes throughout the genome to regulate nucleosome occupancy and
CC chromatin accessibility, and to modulate the expression of target genes
CC (PubMed:25387881). Negative regulator of stress tolerance (e.g. high
CC salt) (PubMed:25387881). {ECO:0000269|PubMed:25387881}.
CC -!- SUBUNIT: Found in a mRNA splicing-dependent exon junction complex (EJC)
CC (PubMed:25387881). Binds specifically histones H3 and H4
CC (PubMed:25387881). Interacts with TOP1A, SCC3, At1g61730, At1g20940,
CC At1g13930, DEK4, HDT1, NIT1, SHL, CYP19-1, GEBPL, HSP70-3, PDP2, PDP3,
CC KIN2, RPL11A and PDS5A (PubMed:25387881).
CC {ECO:0000269|PubMed:25387881}.
CC -!- INTERACTION:
CC Q9SUA1; O82265: SCC3; NbExp=2; IntAct=EBI-1787282, EBI-9397077;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:25387881}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:15496452}. Note=Associates with chromatin
CC (PubMed:25387881). Enriched in regions where chromatin is decondensed
CC or sparse in the interphase nuclei (By similarity).
CC {ECO:0000250|UniProtKB:P35659, ECO:0000269|PubMed:25387881}.
CC -!- TISSUE SPECIFICITY: Highly expressed in young seedlings.
CC {ECO:0000269|PubMed:25387881}.
CC -!- INDUCTION: Strongly and rapidly down-regulated by salt stress in shoots
CC and roots. {ECO:0000269|PubMed:25387881}.
CC -!- DISRUPTION PHENOTYPE: Increased expression of some target genes (e.g.
CC TOP1A, EFS, MBD9, NUP160, DEK1, BIG, HB-1 and CMT3), but reduced
CC expression of other target genes (e.g. HKL1 and PDS5)
CC (PubMed:25387881). Increased salt stress tolerance leading to a better
CC seed germination in high salt conditions (PubMed:25387881).
CC {ECO:0000269|PubMed:25387881}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM13123.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE98684.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AL078465; CAB43859.1; -; Genomic_DNA.
DR EMBL; AL161565; CAB79518.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85228.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85229.1; -; Genomic_DNA.
DR EMBL; AK226545; BAE98684.1; ALT_FRAME; mRNA.
DR EMBL; AK227843; BAE99821.1; -; mRNA.
DR EMBL; AK229601; BAF01448.1; -; mRNA.
DR EMBL; AK316775; BAH19494.1; -; mRNA.
DR EMBL; AY093124; AAM13123.1; ALT_INIT; mRNA.
DR EMBL; BT008491; AAP37850.1; -; mRNA.
DR PIR; T08929; T08929.
DR RefSeq; NP_001031724.1; NM_001036647.3.
DR RefSeq; NP_194393.3; NM_118797.5.
DR AlphaFoldDB; Q9SUA1; -.
DR SMR; Q9SUA1; -.
DR IntAct; Q9SUA1; 19.
DR STRING; 3702.AT4G26630.2; -.
DR PaxDb; Q9SUA1; -.
DR PRIDE; Q9SUA1; -.
DR ProteomicsDB; 183163; -.
DR EnsemblPlants; AT4G26630.1; AT4G26630.1; AT4G26630.
DR EnsemblPlants; AT4G26630.2; AT4G26630.2; AT4G26630.
DR GeneID; 828770; -.
DR Gramene; AT4G26630.1; AT4G26630.1; AT4G26630.
DR Gramene; AT4G26630.2; AT4G26630.2; AT4G26630.
DR KEGG; ath:AT4G26630; -.
DR Araport; AT4G26630; -.
DR TAIR; locus:2133847; AT4G26630.
DR eggNOG; KOG2266; Eukaryota.
DR HOGENOM; CLU_011980_0_0_1; -.
DR InParanoid; Q9SUA1; -.
DR OMA; TAGRGYQ; -.
DR OrthoDB; 912022at2759; -.
DR PhylomeDB; Q9SUA1; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SUA1; baseline and differential.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003682; F:chromatin binding; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042393; F:histone binding; IDA:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IDA:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IEP:TAIR.
DR GO; GO:2000779; P:regulation of double-strand break repair; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR InterPro; IPR044198; DEK.
DR InterPro; IPR014876; DEK_C.
DR PANTHER; PTHR13468; PTHR13468; 2.
DR Pfam; PF08766; DEK_C; 1.
DR PROSITE; PS51998; DEK_C; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Coiled coil; DNA-binding; Nucleus; Reference proteome;
KW Stress response; Transcription; Transcription regulation.
FT CHAIN 1..763
FT /note="DEK domain-containing chromatin-associated protein
FT 3"
FT /id="PRO_0000453266"
FT DOMAIN 676..731
FT /note="DEK-C"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01342"
FT DNA_BIND 694..708
FT /evidence="ECO:0000250|UniProtKB:P35659"
FT DNA_BIND 723..727
FT /evidence="ECO:0000250|UniProtKB:P35659"
FT REGION 1..324
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 458..681
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 730..763
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 60..96
FT /evidence="ECO:0000255"
FT COILED 214..286
FT /evidence="ECO:0000255"
FT COILED 513..551
FT /evidence="ECO:0000255"
FT COILED 723..753
FT /evidence="ECO:0000255"
FT MOTIF 284..291
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 483..490
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 35..240
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 251..266
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 275..324
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 499..521
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 522..536
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 537..563
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 576..602
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 625..650
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 662..681
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 732..746
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 747..763
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 417
FT /note="K -> E (in Ref. 4; BAH19494)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 763 AA; 85249 MW; D67F4F5BD4DB480B CRC64;
MGEDTKATIE PTANKTTSLE KPSEAMAGKE NAGGKETQEL AKDEDMAEPD NMEIDAQIKK
DDEKAETEDK ESEVKKNEDN AETQKMEEKV EVTKDEGQAE ATNMDEDADG KKEQTDDGVS
VEDTVMKENV ESKDNNYAKD DEKETKETDI TEADHKKAGK EDIQHEADKA NGTKDGNTGD
IKEEGTLVDE DKGTDMDEKV ENGDENKQVE NVEGKEKEDK EENKTKEVEA AKAEVDESKV
EDEKEGSEDE NDNEKVESKD AKEDEKEETN DDKEDEKEES KGSKKRGKGT SSGGKVREKN
KTEEVKKDAE PRTPFSDRPV RERKSVERLV ALIDKDSSKE FRVEKGRGAY LKDIPNVANK
VMRKRSDETL KLLHPILFGG RRGKAAQIKT NILGFSGFVW HGDEKKAKEK VKEKLEKCTK
EKLWEFCDVL DIHITKATTK KEDIITKLFE FLEKPHVTGD VTGDTTVSEK EKSSKGAKRK
RTPKKTSPTA GSSSSKRSAK SQKKSEEATK VVKKSLAHSD DESEEEKEEE EKQEEEKAEE
KEEKKEEENE NGIPDKSEDE APQPSESEEK DESEEHSEEE TTKKKRGSRL SAGKKESAGR
ARNKKAVVAA KSSPPEKITQ KRSSAKRKKT DDDSDTSPKA SSKRKKSENP IKASPAPSKS
ASKEKPVKRA GKGKDKPSDK VLKNAIVEIL KRVDFSTATF TDILKELAKE FTEDLTPRKS
SIKMIIQEEL TKLADEEEEE EKKEEDSEKE EAGGSGGGEE VKA
