LDL1_ORYSJ
ID LDL1_ORYSJ Reviewed; 849 AA.
AC Q6Z690; A0A0N7KG44;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Lysine-specific histone demethylase 1 homolog 1;
DE EC=1.-.-.-;
DE AltName: Full=Flavin-containing amine oxidase domain-containing protein 1;
DE AltName: Full=Protein LSD1-LIKE 1;
GN OrderedLocusNames=Os02g0755200, LOC_Os02g51880; ORFNames=P0627E03.23;
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=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 [2]
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 [3]
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 [4]
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; AP005012; BAD17247.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF10075.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS80985.1; -; Genomic_DNA.
DR EMBL; AK070699; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015623199.1; XM_015767713.1.
DR AlphaFoldDB; Q6Z690; -.
DR SMR; Q6Z690; -.
DR STRING; 4530.OS02T0755200-01; -.
DR PaxDb; Q6Z690; -.
DR PRIDE; Q6Z690; -.
DR EnsemblPlants; Os02t0755200-01; Os02t0755200-01; Os02g0755200.
DR GeneID; 4330771; -.
DR Gramene; Os02t0755200-01; Os02t0755200-01; Os02g0755200.
DR KEGG; osa:4330771; -.
DR eggNOG; KOG0029; Eukaryota.
DR HOGENOM; CLU_004498_5_0_1; -.
DR InParanoid; Q6Z690; -.
DR OMA; SSRGEMF; -.
DR OrthoDB; 1034142at2759; -.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; Q6Z690; OS.
DR GO; GO:0005737; C:cytoplasm; IEA:EnsemblPlants.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0016575; P:histone deacetylation; IEA:EnsemblPlants.
DR GO; GO:0051568; P:histone H3-K4 methylation; IEA:EnsemblPlants.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IEA:EnsemblPlants.
DR GO; GO:0048364; P:root development; IEA:EnsemblPlants.
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..849
FT /note="Lysine-specific histone demethylase 1 homolog 1"
FT /id="PRO_0000342896"
FT DOMAIN 159..260
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT REGION 1..118
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..83
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 300
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 302
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 308
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 688
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT CONFLICT 322
FT /note="P -> H (in Ref. 4; AK070699)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 849 AA; 90748 MW; 47F401BCE0ED1BDB CRC64;
MEEGSEAQPP LQPEAVSAEA SEPPPPVPMD QDEGQAAAAE AMEGEAEGAA AAAGTIEGEA
GYAAADADPM EDEAADEAGA AEPMEDDPPT SSAPSATAAV DDSTIARKRR RRKKQFPGMI
PTAGVRVLRA AASAPSAAHL NGVPRRRGRP PTSSSLRLAR ELDAEALIAL AAGFPADSLS
EDEVAAAVLP RIGGVDQTNY LVVRNHVLAL WRSNPLSPVA SNAALASIRA EHAHLVAAAH
SFLSDHAYIN FGLAPSVISL PPCPPPSLPP PSVLIVGAGF AGLAAARHLM SLGFKVAIVE
GRLRPGGRVF TKSMRSTAAE YPDIAAAADL GGSVLTGING NPLGVIARQL GFPLHKVRDK
CPLYLPDGRP VDPDMDARVE AAFNQLLDKV CQLRQVVADS IPHGVDVSLG MALEAFRAAH
GVAAEREERM LLDWHLANLE YANAAPLVDL SMAFWDQDDP YEMGGDHCFI PGGNSRFVRA
LADGIPIFYG QNVRRIQYGC DGAMVYTDKQ TFRGDMVLCT VPLGVLKKGN IQFVPELPAQ
KREAIERLGF GLLNKVVLLF PYDFWDGRID TFGHLTEDSG QRGEFFLFYS YSSVSGGPLL
IALVAGESAI EFEKTSPAEN VEKVLETLRK IFSPKGIEVP KPLQAICTRW GTDKFTYGSY
SYVAIGSSGD DYDILAESVC DRVFFAGEAT NRRYPATMHG ALLSGYREAA NIVRAARRRA
KKVDSPKKMD VNNEVKYEVK VDNIDLDDLF RTPDAAFGGF SVLHDPSTSE PDSISLLRVG
IGARKLGSGS LFLYGLIMRK NVANLAAMEG DEQRLSTLYR DFGTKLVGLD GLGDSGSSLI
SRIKAAARK
