LDL1_ARATH
ID LDL1_ARATH Reviewed; 844 AA.
AC Q8VXV7; Q56WM3; Q9SI68;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Lysine-specific histone demethylase 1 homolog 1 {ECO:0000303|PubMed:17921315};
DE Short=Lysine-specific histone demethylase 1C {ECO:0000303|PubMed:21690391};
DE EC=1.-.-.- {ECO:0000305};
DE AltName: Full=Flavin-containing amine oxidase domain-containing protein 1;
DE AltName: Full=Protein LSD1-LIKE 1 {ECO:0000303|PubMed:17921315, ECO:0000303|PubMed:25852712};
DE Short=AtLSD1 {ECO:0000303|PubMed:17921315};
DE AltName: Full=Protein SWIRM-PAO 1 {ECO:0000303|PubMed:17224141};
DE Short=AtSWP1 {ECO:0000303|PubMed:17224141};
GN Name=LDL1 {ECO:0000303|PubMed:17921315, ECO:0000303|PubMed:25852712};
GN Synonyms=KDM1C {ECO:0000303|PubMed:21690391},
GN LSD1 {ECO:0000303|PubMed:17921315}, SWP1 {ECO:0000303|PubMed:17224141};
GN OrderedLocusNames=At1g62830 {ECO:0000312|Araport:AT1G62830};
GN ORFNames=F23N19.19 {ECO:0000312|EMBL:AAF19542.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 478-844.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP INTERACTION WITH CZS.
RC STRAIN=cv. Columbia;
RX PubMed=17224141; DOI=10.1016/j.ydbio.2006.11.012;
RA Krichevsky A., Gutgarts H., Kozlovsky S.V., Tzfira T., Sutton A.,
RA Sternglanz R., Mandel G., Citovsky V.;
RT "C2H2 zinc finger-SET histone methyltransferase is a plant-specific
RT chromatin modifier.";
RL Dev. Biol. 303:259-269(2007).
RN [6]
RP FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
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 [7]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH OTU6/OTLD1, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=21690391; DOI=10.1073/pnas.1014030108;
RA Krichevsky A., Zaltsman A., Lacroix B., Citovsky V.;
RT "Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone
RT deubiquitinase complexes in plant gene repression.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:11157-11162(2011).
RN [8]
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). In
CC association with OTU6/OTLD1, involved in transcriptional gene
CC repression via histone deubiquitination and demethylation
CC (PubMed:21690391). {ECO:0000269|PubMed:17921315,
CC ECO:0000269|PubMed:21690391, ECO:0000269|PubMed:25852712}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000305};
CC -!- SUBUNIT: Interacts with CZS (PubMed:17224141). Interacts with
CC OTU6/OTLD1 (PubMed:21690391). {ECO:0000269|PubMed:17224141,
CC ECO:0000269|PubMed:21690391}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:21690391}. Cytoplasm {ECO:0000269|PubMed:21690391}.
CC -!- TISSUE SPECIFICITY: Expressed in the shoot and root apical regions of
CC young seedlings. Expressed in cotyledons and inflorescences.
CC {ECO:0000269|PubMed:17921315}.
CC -!- DISRUPTION PHENOTYPE: Up-regulated expression of GLP2A/GLP5A due to
CC derepression associated with hyperubiquitination of the target
CC chromatin and H3K4 hypermethylation. {ECO:0000269|PubMed:21690391}.
CC -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF19542.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 3 genes: At1g62810, At1g62820 and At1g62830.; Evidence={ECO:0000305};
CC Sequence=BAD94669.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC007190; AAF19542.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE34010.1; -; Genomic_DNA.
DR EMBL; AY074561; AAL67101.1; -; mRNA.
DR EMBL; AY143912; AAN28851.1; -; mRNA.
DR EMBL; AK222014; BAD94669.1; ALT_INIT; mRNA.
DR RefSeq; NP_176471.1; NM_104961.4.
DR AlphaFoldDB; Q8VXV7; -.
DR SMR; Q8VXV7; -.
DR BioGRID; 27803; 5.
DR IntAct; Q8VXV7; 3.
DR STRING; 3702.AT1G62830.1; -.
DR iPTMnet; Q8VXV7; -.
DR PaxDb; Q8VXV7; -.
DR PRIDE; Q8VXV7; -.
DR ProteomicsDB; 237132; -.
DR EnsemblPlants; AT1G62830.1; AT1G62830.1; AT1G62830.
DR GeneID; 842582; -.
DR Gramene; AT1G62830.1; AT1G62830.1; AT1G62830.
DR KEGG; ath:AT1G62830; -.
DR Araport; AT1G62830; -.
DR TAIR; locus:2026187; AT1G62830.
DR eggNOG; KOG0029; Eukaryota.
DR HOGENOM; CLU_004498_5_0_1; -.
DR InParanoid; Q8VXV7; -.
DR OMA; SSRGEMF; -.
DR OrthoDB; 1034142at2759; -.
DR PhylomeDB; Q8VXV7; -.
DR BioCyc; ARA:AT1G62830-MON; -.
DR BRENDA; 1.14.99.66; 399.
DR PRO; PR:Q8VXV7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8VXV7; baseline and differential.
DR Genevisible; Q8VXV7; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
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; IMP:TAIR.
DR GO; GO:0051568; P:histone H3-K4 methylation; IMP:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0048364; P:root development; 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; Cytoplasm; FAD; Flavoprotein; Nucleus; Oxidoreductase;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..844
FT /note="Lysine-specific histone demethylase 1 homolog 1"
FT /id="PRO_0000342893"
FT DOMAIN 154..255
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT REGION 1..131
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 516..523
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 1..18
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 44..78
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 106..120
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 295
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 297
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 303
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
FT BINDING 679
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:O60341"
SQ SEQUENCE 844 AA; 93312 MW; 90109850DA90CBA4 CRC64;
MSTETKETRP ETKPEDLGTH TTVDVPGEEP LGELIADDVN EVVSDASATE TDFSLSPSQS
EQNIEEDGQN SLDDQSPLTE LQPLPLPPPL PVEARISESL GEEESSDLVT EQQSQNPNAA
EPGPRARKRR RRKRFFTEIN ANPAFSRNRR TSVGKEVDSE ALIAMSVGFP VYSLTEEEIE
ANVVSIIGGK DQANYIVVRN HIIALWRSNV SNWLTRDHAL ESIRAEHKTL VDTAYNFLLE
HGYINFGLAP VIKEAKLRSF DGVEPPNVVV VGAGLAGLVA ARQLLSMGFR VLVLEGRDRP
GGRVKTRKMK GGDGVEAMAD VGGSVLTGIN GNPLGVLARQ LGLPLHKVRD ICPLYLPNGE
LADASVDSKI EASFNKLLDR VCKLRQSMIE ENKSVDVPLG EALETFRLVY GVAEDQQERM
LLDWHLANLE YANATLLGNL SMAYWDQDDP YEMGGDHCFI PGGNEIFVHA LAENLPIFYG
STVESIRYGS NGVLVYTGNK EFHCDMALCT VPLGVLKKGS IEFYPELPHK KKEAIQRLGF
GLLNKVAMLF PCNFWGEEID TFGRLTEDPS TRGEFFLFYS YSSVSGGPLL VALVAGDAAE
RFETLSPTDS VKRVLQILRG IYHPKGIVVP DPVQALCSRW GQDKFSYGSY SYVAVGSSGD
DYDILAESVG DGRVFFAGEA TNRQYPATMH GAFLSGMREA ANILRVARRR ASSSALNPNQ
ICIDKEEEVD EEEDRCLDQL FETPDLTFGN FSVLFTPNSD EPESMSLLRV RIQMEKPESG
LWLYGLVTRK QAIELGEMDG DELRNEYLRE KLGLVPVERK SLSQEGESMI SSLKAARLNR
QIFD
