D53_ORYSJ
ID D53_ORYSJ Reviewed; 1131 AA.
AC Q2RBP2; B9G8Z0; Q0IV93;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=Protein DWARF 53 {ECO:0000303|PubMed:24336200};
GN Name=D53 {ECO:0000303|PubMed:24336200};
GN OrderedLocusNames=Os11g0104300 {ECO:0000312|EMBL:BAF27372.2},
GN LOC_Os11g01330 {ECO:0000312|EMBL:ABA91056.1};
GN ORFNames=OsJ_32651 {ECO:0000312|EMBL:EEE51496.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, MUTAGENESIS OF
RP 812-ARG--ILE-817, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INDUCTION BY
RP STRIGOLACTONE, UBIQUITINATION, EAR MOTIF, INTERACTION WITH D14; D3; TPR1;
RP TPR2 AND TPR3, AND GENE FAMILY.
RX PubMed=24336200; DOI=10.1038/nature12870;
RA Jiang L., Liu X., Xiong G., Liu H., Chen F., Wang L., Meng X., Liu G.,
RA Yu H., Yuan Y., Yi W., Zhao L., Ma H., He Y., Wu Z., Melcher K., Qian Q.,
RA Xu H.E., Wang Y., Li J.;
RT "DWARF 53 acts as a repressor of strigolactone signalling in rice.";
RL Nature 504:401-405(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, MUTAGENESIS OF 812-ARG--ILE-817, EAR
RP MOTIF, TISSUE SPECIFICITY, INDUCTION BY STRIGOLACTONE, SUBCELLULAR
RP LOCATION, INTERACTION WITH D14, AND DOMAIN.
RX PubMed=24336215; DOI=10.1038/nature12878;
RA Zhou F., Lin Q., Zhu L., Ren Y., Zhou K., Shabek N., Wu F., Mao H.,
RA Dong W., Gan L., Ma W., Gao H., Chen J., Yang C., Wang D., Tan J.,
RA Zhang X., Guo X., Wang J., Jiang L., Liu X., Chen W., Chu J., Yan C.,
RA Ueno K., Ito S., Asami T., Cheng Z., Wang J., Lei C., Zhai H., Wu C.,
RA Wang H., Zheng N., Wan J.;
RT "D14-SCF(D3)-dependent degradation of D53 regulates strigolactone
RT signalling.";
RL Nature 504:406-410(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [8]
RP REVIEW.
RX PubMed=25179782; DOI=10.1016/j.pbi.2014.08.001;
RA Bennett T., Leyser O.;
RT "Strigolactone signalling: standing on the shoulders of DWARFs.";
RL Curr. Opin. Plant Biol. 22:7-13(2014).
RN [9]
RP INTERACTION WITH D14.
RX PubMed=25713176; DOI=10.1093/pcp/pcv028;
RA Umehara M., Cao M., Akiyama K., Akatsu T., Seto Y., Hanada A., Li W.,
RA Takeda-Kamiya N., Morimoto Y., Yamaguchi S.;
RT "Structural requirements of strigolactones for shoot branching inhibition
RT in rice and Arabidopsis.";
RL Plant Cell Physiol. 56:1059-1072(2015).
RN [10]
RP FUNCTION, AND INTERACTION WITH SPL14.
RX PubMed=28809396; DOI=10.1038/cr.2017.102;
RA Song X., Lu Z., Yu H., Shao G., Xiong J., Meng X., Jing Y., Liu G.,
RA Xiong G., Duan J., Yao X.F., Liu C.M., Li H., Wang Y., Li J.;
RT "IPA1 functions as a downstream transcription factor repressed by D53 in
RT strigolactone signaling in rice.";
RL Cell Res. 27:1128-1141(2017).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 794-808.
RX PubMed=28630893; DOI=10.1126/sciadv.1601217;
RA Ma H., Duan J., Ke J., He Y., Gu X., Xu T.H., Yu H., Wang Y.,
RA Brunzelle J.S., Jiang Y., Rothbart S.B., Xu H.E., Li J., Melcher K.;
RT "A D53 repression motif induces oligomerization of TOPLESS corepressors and
RT promotes assembly of a corepressor-nucleosome complex.";
RL Sci. Adv. 3:e1601217-e1601217(2017).
CC -!- FUNCTION: Repressor of strigolactones (SL) signaling (PubMed:24336200,
CC PubMed:24336215). Subjected to a negative feedback control of SL
CC signaling (PubMed:24336200, PubMed:24336215). Suppresses the
CC transcriptional activation activity of SPL14/IPA1 in SL signaling
CC (PubMed:28809396). Acts with SPL14/IPA1 to mediate the SL-regulated
CC tiller development (PubMed:28809396). Subject to a negative feedback
CC regulation by SPL14/IPA1, which binds to D53 promoter to repress D53
CC gene expression (PubMed:28809396). {ECO:0000269|PubMed:24336200,
CC ECO:0000269|PubMed:24336215, ECO:0000269|PubMed:28809396}.
CC -!- SUBUNIT: Interacts with D3 (PubMed:24336200). Interacts with D14
CC (PubMed:24336200, PubMed:25713176). The interaction with D14 is
CC enhanced in the presence of strigolactones (PubMed:24336200). The
CC interaction with D14 occurs in the presence of (2'R) stereoisomers of
CC strigolactones, but not (2'S) stereoisomers (PubMed:25713176).
CC Interacts with the TOPLESS-related proteins TPR1, TPR2 and TPR3
CC (PubMed:24336200). Interacts with SPL14/IPA1 (PubMed:28809396).
CC {ECO:0000269|PubMed:24336200, ECO:0000269|PubMed:24336215,
CC ECO:0000269|PubMed:25713176, ECO:0000269|PubMed:28809396}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24336200,
CC ECO:0000269|PubMed:24336215}.
CC -!- TISSUE SPECIFICITY: Expressed in the shoot bases of seedlings, young
CC leaves, axillary buds and young panicles (PubMed:24336200,
CC PubMed:24336215). Expressed in young roots vasculature, culms,
CC internodes and nodes, preferentially in the parenchyma cells
CC surrounding the xylem (PubMed:24336215). {ECO:0000269|PubMed:24336200,
CC ECO:0000269|PubMed:24336215}.
CC -!- INDUCTION: Up-regulated by strigolactone treatment.
CC {ECO:0000269|PubMed:24336200, ECO:0000269|PubMed:24336215}.
CC -!- DOMAIN: Contains 3 EAR motifs associated with active repression of
CC several target genes (PubMed:24336200, PubMed:24336215). The D1 domain
CC (195-440) is essential for the strigolactone-dependent D53-D14
CC interaction (PubMed:24336215). {ECO:0000269|PubMed:24336215,
CC ECO:0000305|PubMed:24336200}.
CC -!- PTM: Polyubiquitinated. Strigolactone, but not karrikin, triggers rapid
CC SCF(D3)-dependent degradation via the proteasome.
CC {ECO:0000269|PubMed:24336200}.
CC -!- SIMILARITY: Belongs to the ClpA/ClpB family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF27372.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAT12295.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=EEE51496.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; KF623088; AHC72433.1; -; Genomic_DNA.
DR EMBL; KF709434; AHC31003.1; -; mRNA.
DR EMBL; DP000010; ABA91056.1; -; Genomic_DNA.
DR EMBL; AP008217; BAF27372.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014967; BAT12295.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CM000148; EEE51496.1; ALT_SEQ; Genomic_DNA.
DR RefSeq; XP_015617462.1; XM_015761976.1.
DR PDB; 5J9K; X-ray; 2.55 A; C/D=794-808.
DR PDB; 5JA5; X-ray; 2.00 A; B=794-808.
DR PDB; 5JHP; X-ray; 3.15 A; E=794-808.
DR PDBsum; 5J9K; -.
DR PDBsum; 5JA5; -.
DR PDBsum; 5JHP; -.
DR AlphaFoldDB; Q2RBP2; -.
DR SMR; Q2RBP2; -.
DR STRING; 39947.Q2RBP2; -.
DR PaxDb; Q2RBP2; -.
DR PRIDE; Q2RBP2; -.
DR EnsemblPlants; Os11t0104300-01; Os11t0104300-01; Os11g0104300.
DR GeneID; 4349543; -.
DR Gramene; Os11t0104300-01; Os11t0104300-01; Os11g0104300.
DR KEGG; osa:4349543; -.
DR OrthoDB; 182446at2759; -.
DR PlantReactome; R-OSA-5654828; Strigolactone signaling.
DR Proteomes; UP000000763; Chromosome 11.
DR Proteomes; UP000007752; Chromosome 11.
DR Proteomes; UP000059680; Chromosome 11.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:1902347; P:response to strigolactone; IDA:UniProtKB.
DR Gene3D; 1.10.1780.10; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR036628; Clp_N_dom_sf.
DR InterPro; IPR004176; Clp_R_dom.
DR InterPro; IPR027417; P-loop_NTPase.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51903; CLP_R; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Reference proteome; Repeat; Ubl conjugation.
FT CHAIN 1..1131
FT /note="Protein DWARF 53"
FT /id="PRO_0000435718"
FT DOMAIN 8..181
FT /note="Clp R"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 12..85
FT /note="Repeat 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 103..181
FT /note="Repeat 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 511..574
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 588..655
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 951..970
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 976..1002
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 578..582
FT /note="EAR 1"
FT /evidence="ECO:0000305|PubMed:24336200,
FT ECO:0000305|PubMed:24336215"
FT MOTIF 799..803
FT /note="EAR 2"
FT /evidence="ECO:0000305|PubMed:24336200,
FT ECO:0000305|PubMed:24336215"
FT MOTIF 976..981
FT /note="EAR 3"
FT /evidence="ECO:0000305|PubMed:24336200,
FT ECO:0000305|PubMed:24336215"
FT COMPBIAS 554..574
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 596..614
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 812..817
FT /note="RGKTGI->T: In d53; dwarf plants with increased
FT tiller numbers. No effect on the interaction with D14."
FT /evidence="ECO:0000269|PubMed:24336200,
FT ECO:0000269|PubMed:24336215"
SQ SEQUENCE 1131 AA; 122532 MW; 41F0528DB977872F CRC64;
MPTPVAAARQ CLSPAAVPAL DAAVASSRRR AHAQTTSLHL ISSLLAPPAP PLLRDALARA
RSAAYSPRVQ LKALDLCFAV SLDRLPSVSA SSSSSGAADE PPVSNSLMAA IKRSQANQRR
NPDTFHFYHQ AATAQTPAAV KVELSHLVLA ILDDPVVSRV FAEAGFRSGD IKLAILRPAP
PMPLLGRLPT RTRPPPLFLC SFAAADDADV PSPAGNLAGA GEENCRRIAE ILSRGRNPML
VGVGAASAAD DFAAASPYRI IHVDPNTIDR SDLGVAAAMA SATSGLIISI GDLKQLVPDE
DAEAQEKGRR VVAEVTRVLE THSKVGRVWV MGWSATYETY LAFLSKFPLV DKDWDLQLLP
ITAVHAAATA GPAAAAAGLM PPATTVAAFS KPAASLMDSF VPFGGFLCDN YEENSLTANS
CPQALRCQQC NDKYEQEVAT IISASGITAE DHHQGGLPSL LQNGSMMGPN NGFDPVKARD
DRMVLNSKIL NLRKKWNEYC LRLHQDHQRI NRDPYKPFPR YIGVPTDKER SANSSKGSES
VGVQKDVIKP CAVSAVHSSS TARPISSPSV TNKRNEDLVL NLQARHSKSD ENLQERGMQS
QHGTLSNVDN PDDHVSPSSA APVETDLVLG TPRECSSKGS SSTCSKRVED SERSVHLVPK
KVDDLNLKHP QLSVQPNSCS WSSINVGKTS HSTLHSVASG GFSAFGQWQK RSPLAAQNSD
LSNYKLLVER LFKVVGRQEE ALSAICESIV RCRSTESRRG PNRNDIWLCF HGSDSMAKKR
IAVALAELMH GSKDNLIYLD LNLQDWDDSS FRGKTGIDCI VEQLSKKRQS VLFLDNIDRA
DCLVQDSLSD AIKSGRFQDM RGKVVDINDS IVVLSRSMIQ GSKNGLEEGL SFSEEKILAT
RGHRLKILVE PGRAITSGCP SGKVVVSPRH FLTKIQASLC SGSISKRKLS ISDDQEKLQE
SPSSSKRLHR TSSVPFDLNL PVDEDEPLDA DDDSSSHENS YGNTEKSIDA LLHSVDGSIN
FKPFDFDKLA DDMLQEFSNI LRKNLGSECM LEIDVGAMEQ ILAAAWKSEE DRKPVPTWLE
QVFARSLDEL KLKRKHVSSS TLRLVACEDT VPAVKGDGLG VLLPPRIILD C
