DA1_ARATH
ID DA1_ARATH Reviewed; 532 AA.
AC P0C7Q8; Q9LM99;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Protein DA1;
DE AltName: Full=Protein SUPPRESSOR OF LARGE SEED AND ORGAN PHENOTYPES OF DA1-1 1;
GN Name=DA1; Synonyms=SOD1; OrderedLocusNames=At1g19270; ORFNames=T29M8.14;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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].
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [4]
RP FUNCTION, MUTAGENESIS OF ARG-358 AND LEU-362, DISRUPTION PHENOTYPE,
RP INDUCTION BY ABA, DEVELOPMENTAL STAGE, INTERACTION WITH UBIQUITIN, GENE
RP FAMILY, AND NOMENCLATURE.
RX PubMed=18483219; DOI=10.1101/gad.463608;
RA Li Y., Zheng L., Corke F., Smith C., Bevan M.W.;
RT "Control of final seed and organ size by the DA1 gene family in Arabidopsis
RT thaliana.";
RL Genes Dev. 22:1331-1336(2008).
RN [5]
RP FUNCTION, AND INTERACTION WITH DA2.
RX PubMed=24045020; DOI=10.1105/tpc.113.115063;
RA Xia T., Li N., Dumenil J., Li J., Kamenski A., Bevan M.W., Gao F., Li Y.;
RT "The ubiquitin receptor DA1 interacts with the E3 ubiquitin ligase DA2 to
RT regulate seed and organ size in Arabidopsis.";
RL Plant Cell 25:3347-3359(2013).
RN [6]
RP FUNCTION, AND INTERACTION WITH UBP15.
RX PubMed=24585836; DOI=10.1105/tpc.114.122663;
RA Du L., Li N., Chen L., Xu Y., Li Y., Zhang Y., Li C., Li Y.;
RT "The ubiquitin receptor DA1 regulates seed and organ size by modulating the
RT stability of the ubiquitin-specific protease UBP15/SOD2 in Arabidopsis.";
RL Plant Cell 26:665-677(2014).
RN [7]
RP FUNCTION, INTERACTION WITH UBIQUITIN; TCP14 AND TCP15, AND DOMAIN.
RX PubMed=25757472; DOI=10.1105/tpc.114.132274;
RA Peng Y., Chen L., Lu Y., Wu Y., Dumenil J., Zhu Z., Bevan M.W., Li Y.;
RT "The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate
RT endoreduplication by modulating the stability of TCP14/15 in Arabidopsis.";
RL Plant Cell 27:649-662(2015).
RN [8]
RP FUNCTION, UBIQUITINATION AT LYS-95; LYS-221; LYS-348; LYS-376; LYS-381;
RP LYS-391; LYS-474; LYS-475 AND LYS-519, IDENTIFICATION BY MASS SPECTROMETRY,
RP INTERACTION WITH BB, DOMAIN, AND MUTAGENESIS OF ALA-77; SER-81; ALA-109;
RP SER-113; HIS-418 AND HIS-422.
RX PubMed=28167503; DOI=10.1101/gad.292235.116;
RA Dong H., Dumenil J., Lu F.H., Na L., Vanhaeren H., Naumann C., Klecker M.,
RA Prior R., Smith C., McKenzie N., Saalbach G., Chen L., Xia T., Gonzalez N.,
RA Seguela M., Inze D., Dissmeyer N., Li Y., Bevan M.W.;
RT "Ubiquitylation activates a peptidase that promotes cleavage and
RT destabilization of its activating E3 ligases and diverse growth regulatory
RT proteins to limit cell proliferation in Arabidopsis.";
RL Genes Dev. 31:197-208(2017).
RN [9]
RP FUNCTION.
RX PubMed=28003326; DOI=10.1104/pp.16.01410;
RA Vanhaeren H., Nam Y.J., De Milde L., Chae E., Storme V., Weigel D.,
RA Gonzalez N., Inze D.;
RT "Forever young: the role of ubiquitin receptor DA1 and E3 ligase BIG
RT BROTHER in controlling leaf growth and development.";
RL Plant Physiol. 173:1269-1282(2017).
CC -!- FUNCTION: Ubiquitin receptor that limits final seed and organ size by
CC restricting the period of cell proliferation. May act maternally to
CC control seed mass (PubMed:18483219, PubMed:24045020). Acts
CC synergistically with DA2 to regulate seed size. Functions
CC synergistically with DA2 to restrict cell proliferation in the maternal
CC integuments of ovules and developing seeds (PubMed:24045020). Functions
CC antagonistically in a common pathway with UBP15 to regulate seed size.
CC Associates physically with UBP15 and modulates the stability of UBP15,
CC which promote cell proliferation in the integuments of ovules and
CC developing seeds (PubMed:24585836). Functions as peptidase and cleaves
CC the N-terminal sequence of E3 ubiquitin-protein ligases BB and DA2 in a
CC ubiquitin-dependent manner. Cleaves the deubiquitinating enzyme UBP15,
CC which promotes cell proliferation, and the transcription factors TCP15
CC and TCP22, which promote cell proliferation and repress
CC endoreduplication (PubMed:28167503). Involved in the promotion of leaf
CC senescence, in addition to its function in restricting plant growth
CC (PubMed:28003326). Acts redundantly with DAR1 and DAR2 to regulate
CC endoreduplication during leaf development. Together with DAR1 and DAR2,
CC modulates the protein stability of the transcription factors TCP14 and
CC TCP15, which repress endoreduplication by directly regulating the
CC expression of cell-cycle genes (PubMed:25757472).
CC {ECO:0000269|PubMed:18483219, ECO:0000269|PubMed:24045020,
CC ECO:0000269|PubMed:24585836, ECO:0000269|PubMed:25757472,
CC ECO:0000269|PubMed:28003326, ECO:0000269|PubMed:28167503}.
CC -!- SUBUNIT: Interacts with ubiquitin (PubMed:18483219, PubMed:25757472).
CC Interacts (via C-terminus) with DA2 (PubMed:24045020). Interacts with
CC BB (PubMed:28167503). Interacts with UBP15 (PubMed:24585836). Interacts
CC with TCP14 and TCP15 (PubMed:25757472). {ECO:0000269|PubMed:18483219,
CC ECO:0000269|PubMed:24045020, ECO:0000269|PubMed:24585836,
CC ECO:0000269|PubMed:25757472, ECO:0000269|PubMed:28167503}.
CC -!- DEVELOPMENTAL STAGE: Highly expressed during the early stages of leaf,
CC petal, integument, and embryo formation and fade away later in petal
CC and leaf development. {ECO:0000269|PubMed:18483219}.
CC -!- INDUCTION: Induced by abscisic acid (ABA).
CC {ECO:0000269|PubMed:18483219}.
CC -!- DOMAIN: The UIM domains bind molecules modified by monoubiquitin or
CC ubiquitin chains and promote coupled monoubiquitination.
CC {ECO:0000305|PubMed:25757472, ECO:0000305|PubMed:28167503}.
CC -!- PTM: Ubiquitinated at LYS-95, LYS-221, LYS-348, LYS-376, LYS-381, LYS-
CC 391, LYS-474, LYS-475 and LYS-519 by the E3 ubiquitin-protein ligases
CC BB and DA2. {ECO:0000269|PubMed:28167503}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:18483219}.
CC -!- MISCELLANEOUS: 'Da' means 'large' in Chinese (PubMed:18483219). Plants
CC overexpressing DA1 exhibit early senescence (PubMed:28003326).
CC {ECO:0000269|PubMed:28003326, ECO:0000303|PubMed:18483219}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF82237.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At1g19270 and At1g19290.; Evidence={ECO:0000305};
CC Sequence=BX816571; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC069143; AAF82237.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE29825.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58072.1; -; Genomic_DNA.
DR EMBL; BX816571; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; D86326; D86326.
DR RefSeq; NP_001320535.1; NM_001332389.1.
DR RefSeq; NP_173361.1; NM_101785.4.
DR AlphaFoldDB; P0C7Q8; -.
DR BioGRID; 23749; 14.
DR IntAct; P0C7Q8; 11.
DR STRING; 3702.AT1G19270.1; -.
DR iPTMnet; P0C7Q8; -.
DR PaxDb; P0C7Q8; -.
DR PRIDE; P0C7Q8; -.
DR ProteomicsDB; 224704; -.
DR EnsemblPlants; AT1G19270.1; AT1G19270.1; AT1G19270.
DR EnsemblPlants; AT1G19270.2; AT1G19270.2; AT1G19270.
DR GeneID; 838510; -.
DR Gramene; AT1G19270.1; AT1G19270.1; AT1G19270.
DR Gramene; AT1G19270.2; AT1G19270.2; AT1G19270.
DR KEGG; ath:AT1G19270; -.
DR Araport; AT1G19270; -.
DR TAIR; locus:2202175; AT1G19270.
DR eggNOG; KOG1703; Eukaryota.
DR HOGENOM; CLU_015906_4_0_1; -.
DR OMA; SCYKELF; -.
DR OrthoDB; 1158670at2759; -.
DR PhylomeDB; P0C7Q8; -.
DR PRO; PR:P0C7Q8; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; P0C7Q8; baseline and differential.
DR Genevisible; P0C7Q8; AT.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008233; F:peptidase activity; IDA:TAIR.
DR GO; GO:0043130; F:ubiquitin binding; IDA:UniProtKB.
DR GO; GO:0008285; P:negative regulation of cell population proliferation; IMP:TAIR.
DR GO; GO:0046621; P:negative regulation of organ growth; IMP:TAIR.
DR GO; GO:0048482; P:plant ovule morphogenesis; IMP:TAIR.
DR GO; GO:1900057; P:positive regulation of leaf senescence; IMP:TAIR.
DR GO; GO:0032875; P:regulation of DNA endoreduplication; IMP:UniProtKB.
DR GO; GO:0046620; P:regulation of organ growth; IMP:UniProtKB.
DR GO; GO:0080113; P:regulation of seed growth; IMP:UniProtKB.
DR GO; GO:0048317; P:seed morphogenesis; IMP:TAIR.
DR InterPro; IPR045218; DA1-like.
DR InterPro; IPR022087; DA1-like_dom.
DR InterPro; IPR003903; UIM_dom.
DR InterPro; IPR001781; Znf_LIM.
DR PANTHER; PTHR24209; PTHR24209; 1.
DR Pfam; PF12315; DA1-like; 1.
DR Pfam; PF00412; LIM; 1.
DR SMART; SM00132; LIM; 1.
DR SMART; SM00726; UIM; 2.
DR PROSITE; PS00478; LIM_DOMAIN_1; 1.
DR PROSITE; PS50023; LIM_DOMAIN_2; 1.
DR PROSITE; PS50330; UIM; 2.
DR PROSITE; PS00142; ZINC_PROTEASE; 1.
PE 1: Evidence at protein level;
KW Developmental protein; Isopeptide bond; LIM domain; Metal-binding;
KW Reference proteome; Repeat; Ubl conjugation; Zinc.
FT CHAIN 1..532
FT /note="Protein DA1"
FT /id="PRO_0000342698"
FT DOMAIN 69..88
FT /note="UIM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00213"
FT DOMAIN 101..120
FT /note="UIM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00213"
FT DOMAIN 170..230
FT /note="LIM zinc-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT REGION 26..71
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 39..58
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CROSSLNK 95
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 221
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 348
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 376
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 381
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 391
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 474
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 475
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT CROSSLNK 519
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 77
FT /note="A->G: No effect on ubiquitin binding; when
FT associated with G-81."
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 81
FT /note="S->G: No effect on ubiquitin binding; when
FT associated with G-77."
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 109
FT /note="A->G: Abolishes binding of ubiquitin; when
FT associated with G-113."
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 113
FT /note="S->G: Abolishes binding of ubiquitin; when
FT associated with G-109."
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 358
FT /note="R->K: In da1-1; increased seed and organ size mainly
FT due to altered numbers of normally sized cells, negative
FT activity toward DA1 and DAR1, but normal fertility.
FT Suppression of large seed and organ phenotypes of da1-1;
FT when associated with F-362."
FT /evidence="ECO:0000269|PubMed:18483219"
FT MUTAGEN 362
FT /note="L->F: In sod1-1; suppression of large seed and organ
FT phenotypes of da1-1; when associated with K-358."
FT /evidence="ECO:0000269|PubMed:18483219"
FT MUTAGEN 418
FT /note="H->A: Abolishes peptidase activity; when associated
FT with A-422."
FT /evidence="ECO:0000269|PubMed:28167503"
FT MUTAGEN 422
FT /note="H->A: Abolishes peptidase activity; when associated
FT with A-418."
FT /evidence="ECO:0000269|PubMed:28167503"
FT CONFLICT 443
FT /note="Q -> S (in Ref. 3; BX816571)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 532 AA; 60364 MW; F13915A7F57D72B5 CRC64;
MGWFNKIFKG SNQRLRVGNN KHNHNVYYDN YPTASHDDEP SAADTDADND EPHHTQEPST
SEDNTSNDQE NEDIDRAIAL SLLEENQEQT SISGKYSMPV DEDEQLARAL QESMVVGNSP
RHKSGSTYDN GNAYGAGDLY GNGHMYGGGN VYANGDIYYP RPITFQMDFR ICAGCNMEIG
HGRFLNCLNS LWHPECFRCY GCSQPISEYE FSTSGNYPFH KACYRERYHP KCDVCSHFIP
TNHAGLIEYR AHPFWVQKYC PSHEHDATPR CCSCERMEPR NTRYVELNDG RKLCLECLDS
AVMDTMQCQP LYLQIQNFYE GLNMKVEQEV PLLLVERQAL NEAREGEKNG HYHMPETRGL
CLSEEQTVST VRKRSKHGTG KWAGNITEPY KLTRQCEVTA ILILFGLPRL LTGSILAHEM
MHAWMRLKGF RTLSQDVEEG ICQVMAHKWL DAELAAGSTN SNAASSSSSS QGLKKGPRSQ
YERKLGEFFK HQIESDASPV YGDGFRAGRL AVHKYGLRKT LEHIQMTGRF PV
