LDL2_ARATH
ID LDL2_ARATH Reviewed; 746 AA.
AC Q9LID0;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Lysine-specific histone demethylase 1 homolog 2 {ECO:0000303|PubMed:17921315};
DE EC=1.-.-.- {ECO:0000305};
DE AltName: Full=Flavin-containing amine oxidase domain-containing protein 2;
DE AltName: Full=Protein LSD1-LIKE 2 {ECO:0000303|PubMed:17921315};
GN Name=LDL2 {ECO:0000303|PubMed:17921315};
GN OrderedLocusNames=At3g13682 {ECO:0000312|Araport:AT3G13682};
GN ORFNames=MMM17.10 {ECO:0000312|EMBL:BAB01917.1};
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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 FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=17921315; DOI=10.1105/tpc.107.052373;
RA Jiang D., Yang W., He Y., Amasino R.M.;
RT "Arabidopsis relatives of the human lysine-specific demethylase1 repress
RT the expression of FWA and FLOWERING LOCUS C and thus promote the floral
RT transition.";
RL Plant Cell 19:2975-2987(2007).
RN [4]
RP FUNCTION.
RX PubMed=25852712; DOI=10.3389/fpls.2015.00159;
RA Zhao M., Yang S., Liu X., Wu K.;
RT "Arabidopsis histone demethylases LDL1 and LDL2 control primary seed
RT dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related
RT genes.";
RL Front. Plant Sci. 6:159-159(2015).
CC -!- FUNCTION: Probable histone demethylase that reduces the levels of
CC histone H3 'Lys-4' methylation in chromatin of the floral repressor
CC FLOWERING LOCUS C (FLC) and the sporophytically silenced floral
CC repressor FWA (PubMed:17921315). Seems to act in partial redundancy
CC with FLOWERING LOCUS D (FLD) to repress FLC expression
CC (PubMed:17921315). Required for cytosine methylation of FWA
CC (PubMed:17921315). Controls primary seed dormancy by regulating DOG1
CC and abscisic acid signaling-related genes (PubMed:25852712).
CC {ECO:0000269|PubMed:17921315, ECO:0000269|PubMed:25852712}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000305};
CC -!- INTERACTION:
CC Q9LID0; Q9ZSY8: IAA27; NbExp=3; IntAct=EBI-15195631, EBI-3946677;
CC -!- TISSUE SPECIFICITY: Expressed in the shoot and root apical regions of
CC young seedlings. Expressed in inflorescences.
CC {ECO:0000269|PubMed:17921315}.
CC -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC {ECO:0000305}.
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DR EMBL; AP001307; BAB01917.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75397.1; -; Genomic_DNA.
DR RefSeq; NP_187981.1; NM_112218.2.
DR AlphaFoldDB; Q9LID0; -.
DR SMR; Q9LID0; -.
DR BioGRID; 5911; 3.
DR IntAct; Q9LID0; 3.
DR STRING; 3702.AT3G13682.1; -.
DR PaxDb; Q9LID0; -.
DR PRIDE; Q9LID0; -.
DR ProteomicsDB; 237133; -.
DR EnsemblPlants; AT3G13682.1; AT3G13682.1; AT3G13682.
DR GeneID; 820577; -.
DR Gramene; AT3G13682.1; AT3G13682.1; AT3G13682.
DR KEGG; ath:AT3G13682; -.
DR Araport; AT3G13682; -.
DR TAIR; locus:2091501; AT3G13682.
DR eggNOG; KOG0029; Eukaryota.
DR HOGENOM; CLU_004498_5_0_1; -.
DR InParanoid; Q9LID0; -.
DR OMA; GNLEYAC; -.
DR OrthoDB; 1034142at2759; -.
DR PhylomeDB; Q9LID0; -.
DR BioCyc; ARA:AT3G13682-MON; -.
DR PRO; PR:Q9LID0; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LID0; baseline and differential.
DR Genevisible; Q9LID0; AT.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0051568; P:histone H3-K4 methylation; IMP:TAIR.
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 1: Evidence at protein level;
KW Chromatin regulator; FAD; Flavoprotein; Oxidoreductase; Reference proteome;
KW Repressor; Transcription; Transcription regulation.
FT CHAIN 1..746
FT /note="Lysine-specific histone demethylase 1 homolog 2"
FT /id="PRO_0000342894"
FT DOMAIN 51..152
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..26
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 189
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 191
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 197
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 569
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
SQ SEQUENCE 746 AA; 82350 MW; E0FD2C0119C4EF00 CRC64;
MNSPASDETA PRRNRRKVSR KNYDENAMDE LIEKQLGGKA KKKYRTKQDL EKETETEALI
ALSVGFPIDE LLEEEIRAGV VRELGGKEQN DYIVVRNHIV ARWRGNVGIW LLKDQIRETV
SSDFEHLISA AYDFLLFNGY INFGVSPLFA PYIPEEGTEG SVIVVGAGLA GLAAARQLLS
FGFKVLVLEG RSRPGGRVYT QKMGGKDRFA AVELGGSVIT GLHANPLGVL ARQLSIPLHK
VRDNCPLYNS EGVLVDKVAD SNVEFGFNKL LDKVTEVREM MEGAAKKISL GEVLETLRVL
YGVAKDSEER KLFDWHLANL EYANAGCLSN LSAAYWDQDD PYEMGGDHCF LAGGNWRLIN
ALAEGLPIIY GKSVDTIKYG DGGVEVISGS QIFQADMILC TVPLGVLKKR SIKFEPELPR
RKQAAIDRLG FGLLNKVAML FPSVFWGDEL DTFGCLNESS INRGEFFLFY AYHTVSGGPA
LVALVAGEAA QRFECTEPSV LLHRVLKKLR GIYGPKGVVV PDPIQTVCTR WGSDPLSYGS
YSHVRVGSSG VDYDILAESV SNRLFFAGEA TTRQHPATMH GAYLSGLREA SKILHVANYL
RSNLKKPVQR YSGVNINVLE DMFKRPDIAI GKLSFVFNPL TDDPKSFGLV RVCFDNFEED
PTNRLQLYTI LSREQANKIK ELDENSNESK LSCLMNTLGL KLMGANSVLD TGGALISVIA
NARRGRSRSH VVAGQCNLPL NPLHFN
