ID   HDR3_ORYSJ              Reviewed;         501 AA.
AC   Q10NJ6; Q0DT56;
DT   23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   03-AUG-2022, entry version 119.
DE   RecName: Full=LIM domain-containing protein HDR3 {ECO:0000305};
DE   AltName: Full=Protein HOMOLOG OF DA1 ON RICE CHROMOSOME 3 {ECO:0000303|PubMed:34323980};
GN   Name=HDR3 {ECO:0000303|PubMed:34323980};
GN   OrderedLocusNames=Os03g0267800 {ECO:0000312|EMBL:BAS83432.1},
GN   LOC_Os03g16090 {ECO:0000312|EMBL:ABF95162.1};
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA   Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA   Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA   Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA   Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA   Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA   Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA   Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA   Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA   Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA   O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA   Jin W., Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT   and diverged grass species.";
RL   Genome Res. 15:1284-1291(2005).
RN   [2]
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   [3]
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   [4]
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   [5]
RP   FUNCTION, INTERACTION WITH GW6A, DOMAIN, AND DISRUPTION PHENOTYPE.
RX   PubMed=34323980; DOI=10.1093/plcell/koab194;
RA   Gao Q., Zhang N., Wang W.Q., Shen S.Y., Bai C., Song X.J.;
RT   "The ubiquitin-interacting motif-type ubiquitin receptor HDR3 interacts
RT   with and stabilizes the histone acetyltransferase GW6a to control the grain
RT   size in rice.";
RL   Plant Cell 33:3331-3347(2021).
CC   -!- FUNCTION: Ubiquitin receptor that functions as a positive regulator of
CC       grain size and weight (PubMed:34323980). Functions in the same genetic
CC       pathway as GW6A to regulate grain size (PubMed:34323980). Modulates
CC       grain size in a similar manner to GW6A, by altering cell proliferation
CC       in spikelet hulls (PubMed:34323980). Interacts with and enhances the
CC       ubiquitination of GW6A (PubMed:34323980). This stabilizes GW6A, delays
CC       protein degradation by the 26S proteasome and enhances GW6A histone
CC       acetyltransferase activity (PubMed:34323980).
CC       {ECO:0000269|PubMed:34323980}.
CC   -!- SUBUNIT: Interacts (via N-terminus) with GW6A (via C-terminus).
CC       {ECO:0000269|PubMed:34323980}.
CC   -!- DOMAIN: The UIM domains bind molecules modified by monoubiquitin or
CC       ubiquitin chains and promote coupled monoubiquitination.
CC       {ECO:0000269|PubMed:34323980}.
CC   -!- DISRUPTION PHENOTYPE: Mutant plants produce grains with reduced size.
CC       {ECO:0000269|PubMed:34323980}.
CC   -!- MISCELLANEOUS: Plants overexpressing HDR3 produces enlarged grains.
CC       {ECO:0000269|PubMed:34323980}.
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DR   EMBL; DP000009; ABF95162.1; -; Genomic_DNA.
DR   EMBL; AP008209; BAF11582.1; -; Genomic_DNA.
DR   EMBL; AP014959; BAS83432.1; -; Genomic_DNA.
DR   RefSeq; XP_015632414.1; XM_015776928.1.
DR   AlphaFoldDB; Q10NJ6; -.
DR   STRING; 4530.OS03T0267800-01; -.
DR   PaxDb; Q10NJ6; -.
DR   PRIDE; Q10NJ6; -.
DR   EnsemblPlants; Os03t0267800-01; Os03t0267800-01; Os03g0267800.
DR   GeneID; 4332368; -.
DR   Gramene; Os03t0267800-01; Os03t0267800-01; Os03g0267800.
DR   eggNOG; KOG1703; Eukaryota.
DR   HOGENOM; CLU_015906_4_0_1; -.
DR   InParanoid; Q10NJ6; -.
DR   OMA; HEATHAF; -.
DR   OrthoDB; 1158670at2759; -.
DR   Proteomes; UP000000763; Chromosome 3.
DR   Proteomes; UP000059680; Chromosome 3.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0043130; F:ubiquitin binding; IBA:GO_Central.
DR   InterPro; IPR045218; DA1-like.
DR   InterPro; IPR022087; DA1-like_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   PROSITE; PS00478; LIM_DOMAIN_1; 1.
DR   PROSITE; PS50023; LIM_DOMAIN_2; 1.
DR   PROSITE; PS00142; ZINC_PROTEASE; 1.
PE   1: Evidence at protein level;
KW   LIM domain; Metal-binding; Reference proteome; Repeat; Zinc.
FT   CHAIN           1..501
FT                   /note="LIM domain-containing protein HDR3"
FT                   /id="PRO_0000454921"
FT   DOMAIN          65..84
FT                   /note="UIM 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00213"
FT   DOMAIN          94..113
FT                   /note="UIM 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00213"
FT   DOMAIN          131..191
FT                   /note="LIM zinc-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT   REGION          33..67
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          429..448
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   501 AA;  57171 MW;  BC863E9D65DED68E CRC64;
     MAYSSRSCDQ CSHERRSGFM KWLCAFLKGT KDGEANRRRP RVTAGEETTL WEEPVRPKKE
     EPPRHNNEEM DHALALALAD DAKNTKERNH DKGENDEELA RAIQDSLNMN PYQPYNPCAP
     SQTQARSRGY RVCGGCKHEI GHGHYLSCLG MYWHPQCFRC SSCRHPIREM EFTLLGTDPY
     HKLCYKELHH PKCDVCLQFI PTNRTGLIEY RAHPFWGQKY CPLHEHDRTP RCCSCEKMEP
     RNTKYMSLGD GRSLCMECLD SAIMDTGECQ PLYHSIRDYY EGMNMKLDQQ IPMLLVERQA
     LNEAMEGESK GPHHMPETRG LCLSEEQTVT SILRRPRIGA NRLLDMKTQP QKLTRRCEVT
     AILVLFGLPR LLTGSILAHE LMHGWLRLKG YRNLKAEIEE GICQVMSYLW LESEILPSTS
     RYGQASTSYA SSSSSSCRPP PSKKGGISHT EKKLGEFFLH QIANDTSSAY GDGFRAAYAA
     VNKYGLRQSL NHIRLTGGFP V