ID   LDL3_ORYSJ              Reviewed;         811 AA.
AC   Q7XUR2;
DT   01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2004, sequence version 2.
DT   03-AUG-2022, entry version 113.
DE   RecName: Full=Lysine-specific histone demethylase 1 homolog 3;
DE            EC=1.-.-.-;
DE   AltName: Full=Flavin-containing amine oxidase domain-containing protein 3;
DE   AltName: Full=Protein FLOWERING LOCUS D-LIKE;
DE   AltName: Full=Protein LSD1-LIKE 3;
GN   OrderedLocusNames=Os04g0560300, LOC_Os04g47270; ORFNames=OSJNBa0084K11.6;
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=12447439; DOI=10.1038/nature01183;
RA   Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA   Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA   Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA   Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA   Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA   Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA   Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA   Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA   Li J., Hong G., Xue Y., Han B.;
RT   "Sequence and analysis of rice chromosome 4.";
RL   Nature 420:316-320(2002).
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   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- FUNCTION: Probable histone demethylase. {ECO:0000250}.
CC   -!- COFACTOR:
CC       Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000305};
CC   -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC       {ECO:0000305}.
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DR   EMBL; AL606687; CAD41075.2; -; Genomic_DNA.
DR   EMBL; AP008210; BAF15459.1; -; Genomic_DNA.
DR   EMBL; AP014960; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AK073751; -; NOT_ANNOTATED_CDS; mRNA.
DR   AlphaFoldDB; Q7XUR2; -.
DR   SMR; Q7XUR2; -.
DR   STRING; 4530.OS04T0560300-01; -.
DR   PaxDb; Q7XUR2; -.
DR   PRIDE; Q7XUR2; -.
DR   eggNOG; KOG0029; Eukaryota.
DR   HOGENOM; CLU_004498_5_0_1; -.
DR   InParanoid; Q7XUR2; -.
DR   Proteomes; UP000000763; Chromosome 4.
DR   Proteomes; UP000059680; Chromosome 4.
DR   Genevisible; Q7XUR2; OS.
DR   GO; GO:0110165; C:cellular anatomical entity; IEA:UniProt.
DR   GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:UniProt.
DR   GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR   GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0016570; P:histone modification; IEA:UniProt.
DR   Gene3D; 1.10.10.10; -; 1.
DR   Gene3D; 3.50.50.60; -; 1.
DR   InterPro; IPR002937; Amino_oxidase.
DR   InterPro; IPR036188; FAD/NAD-bd_sf.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR007526; SWIRM.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   Pfam; PF01593; Amino_oxidase; 1.
DR   Pfam; PF04433; SWIRM; 1.
DR   SUPFAM; SSF46689; SSF46689; 1.
DR   SUPFAM; SSF51905; SSF51905; 1.
DR   PROSITE; PS50934; SWIRM; 1.
PE   2: Evidence at transcript level;
KW   Chromatin regulator; FAD; Flavoprotein; Oxidoreductase; Reference proteome.
FT   CHAIN           1..811
FT                   /note="Lysine-specific histone demethylase 1 homolog 3"
FT                   /id="PRO_0000342899"
FT   DOMAIN          88..189
FT                   /note="SWIRM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT   REGION          1..79
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          790..811
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..36
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         227
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         229
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         235
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         609
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        95
FT                   /note="A -> P (in Ref. 5; AK073751)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        383
FT                   /note="V -> G (in Ref. 5; AK073751)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        399
FT                   /note="S -> A (in Ref. 5; AK073751)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   811 AA;  87396 MW;  50AB190C89B55E9D CRC64;
     MSDQPPPYTP LPLLSSFPPN PYPDQTPDPA STPTLVLPNP AFPNKRKRTG FRRKLPSGSP
     AAPVAVAASP SAQPPPRASA ADDIIVINRE PTAEAVTALT AGFPADSLTD EEIEAGVVSD
     VGGIEQVNYI LIRNHLLTRW RETFNSWLAK ESFATLIPPH CDHLLNAAYS FLVSHGHINF
     GVAPAIKERI PKEPTRHNTV IVVGAGLAGL AAARQLVAFG FKVVVLEGRK RCGGRVYTKK
     MEGGGRSAAG DLGGSVLTGT FGNPLGIVAK QLGLPMHKIR DKCPLYRPDG SPVDPEVDKK
     VEGTFNKLLD KSSLLRASMG DVAMDVSLGA ALETLRQTDG DLSTDQEMNL FNWHLANLEY
     ANAGLLSKLS LAFWDQDDPY DMVGDHCFLP GGNGRLVQSL AENVPIVYER TVHTIRYGGD
     GVQVVVNGGQ VYEGDMALCT VPLGVLKNGG VKFVPELPQR KLDSIKRLGF GLLNKVAMLF
     PHVFWSTDLD TFGHLTEDPS HRGEFFLFYS YATVAGGPLL MALVAGEAAH NFETTPPTDA
     VSSVLKILRG IYEPQGIEVP DPLQSVCTRW GTDSFSLGSY SHVAVGASGD DYDILAESVG
     DGRLFFAGEA TTRRYPATMH GAFISGLREA ANITLHANAR AAKSKVEKGP STNTQACAAL
     LMDLFRQPDL EFGSFSVIFG GQASDPKSPA ILKVELGGPR KKGATEGGKA DQHHSNKLLF
     QQLQSHFNQQ QQLYVYTLLS RQQAMELREV RGGDEMRLHY LCEKLGVKLV GRKGLGPGAD
     AVIASIKAER NSSRTKTRPS KLKIGIPKSK S