LDL3_ARATH
ID LDL3_ARATH Reviewed; 1628 AA.
AC F4JLS1; D2CJC4; O23476; O23477; Q5BPL0;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 68.
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 LSD1-like 3;
GN Name=LDL3; OrderedLocusNames=At4g16310/At4g16320;
GN ORFNames=dl4185w/dl4190w, FCAALL.342/FCAALL.344;
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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 204-1102.
RC STRAIN=cv. Columbia;
RA Krichevsky A., Citovsky V.;
RL Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1321-1536.
RC STRAIN=cv. Columbia;
RA Underwood B.A., Xiao Y.-L., Moskal W.A. Jr., Monaghan E.L., Wang W.,
RA Redman J.C., Wu H.C., Utterback T., Town C.D.;
RL Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION.
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).
CC -!- FUNCTION: Probable histone demethylase that reduces the levels of
CC histone H3 'Lys-4' methylation in chromatin.
CC {ECO:0000269|PubMed:17921315}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000305};
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4JLS1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JLS1-2; Sequence=VSP_055610;
CC -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB10408.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At4g16310 and At4g16320.; Evidence={ECO:0000305};
CC Sequence=CAB10409.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At4g16310 and At4g16320.; Evidence={ECO:0000305};
CC Sequence=CAB78673.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At4g16310 and At4g16320.; Evidence={ECO:0000305};
CC Sequence=CAB78674.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At4g16310 and At4g16320.; Evidence={ECO:0000305};
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DR EMBL; Z97340; CAB10408.1; ALT_SEQ; Genomic_DNA.
DR EMBL; Z97340; CAB10409.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161543; CAB78673.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161543; CAB78674.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83730.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66788.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66789.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66790.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66791.1; -; Genomic_DNA.
DR EMBL; EF442804; ABR13972.1; -; mRNA.
DR EMBL; AY924818; AAX23893.1; -; mRNA.
DR PIR; F71429; F71429.
DR PIR; G71429; G71429.
DR RefSeq; NP_001319957.1; NM_001341093.1. [F4JLS1-1]
DR RefSeq; NP_001328664.1; NM_001341096.1. [F4JLS1-1]
DR RefSeq; NP_001328665.1; NM_001341094.1. [F4JLS1-1]
DR RefSeq; NP_001328666.1; NM_001341095.1. [F4JLS1-1]
DR RefSeq; NP_193364.5; NM_117726.5. [F4JLS1-1]
DR AlphaFoldDB; F4JLS1; -.
DR SMR; F4JLS1; -.
DR STRING; 3702.AT4G16310.1; -.
DR iPTMnet; F4JLS1; -.
DR PaxDb; F4JLS1; -.
DR PRIDE; F4JLS1; -.
DR ProteomicsDB; 237134; -. [F4JLS1-1]
DR EnsemblPlants; AT4G16310.1; AT4G16310.1; AT4G16310. [F4JLS1-1]
DR EnsemblPlants; AT4G16310.2; AT4G16310.2; AT4G16310. [F4JLS1-1]
DR EnsemblPlants; AT4G16310.3; AT4G16310.3; AT4G16310. [F4JLS1-1]
DR EnsemblPlants; AT4G16310.4; AT4G16310.4; AT4G16310. [F4JLS1-1]
DR EnsemblPlants; AT4G16310.5; AT4G16310.5; AT4G16310. [F4JLS1-1]
DR GeneID; 827325; -.
DR Gramene; AT4G16310.1; AT4G16310.1; AT4G16310. [F4JLS1-1]
DR Gramene; AT4G16310.2; AT4G16310.2; AT4G16310. [F4JLS1-1]
DR Gramene; AT4G16310.3; AT4G16310.3; AT4G16310. [F4JLS1-1]
DR Gramene; AT4G16310.4; AT4G16310.4; AT4G16310. [F4JLS1-1]
DR Gramene; AT4G16310.5; AT4G16310.5; AT4G16310. [F4JLS1-1]
DR KEGG; ath:AT4G16310; -.
DR Araport; AT4G16310; -.
DR TAIR; locus:2130454; AT4G16310.
DR eggNOG; KOG0029; Eukaryota.
DR HOGENOM; CLU_001527_1_0_1; -.
DR InParanoid; F4JLS1; -.
DR OMA; TFAMRDH; -.
DR OrthoDB; 1034142at2759; -.
DR PRO; PR:F4JLS1; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JLS1; baseline and differential.
DR Genevisible; F4JLS1; AT.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0046592; F:polyamine oxidase activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016570; P:histone modification; IEA:UniProt.
DR GO; GO:0006598; P:polyamine catabolic process; IBA:GO_Central.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 1.20.930.10; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR002937; Amino_oxidase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR007526; SWIRM.
DR InterPro; IPR035441; TFIIS/LEDGF_dom_sf.
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; SSF47676; SSF47676; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR PROSITE; PS50934; SWIRM; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chromatin regulator; FAD; Flavoprotein;
KW Oxidoreductase; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..1628
FT /note="Lysine-specific histone demethylase 1 homolog 3"
FT /id="PRO_0000430140"
FT DOMAIN 378..478
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT REGION 1..71
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1271..1317
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..19
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 30..71
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1274..1289
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1290..1317
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 647
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 649
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 655
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 1077
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1232..1296
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_055610"
FT CONFLICT 41
FT /note="S -> P (in Ref. 1; CAB10408/CAB78673)"
FT /evidence="ECO:0000305"
FT CONFLICT 70
FT /note="D -> A (in Ref. 1; CAB10408/CAB78673)"
FT /evidence="ECO:0000305"
FT CONFLICT 220
FT /note="H -> D (in Ref. 4; ABR13972 and 1; CAB10408/
FT CAB78673)"
FT /evidence="ECO:0000305"
FT CONFLICT 1042
FT /note="D -> E (in Ref. 4; ABR13972 and 1; CAB10408/
FT CAB78673)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1628 AA; 179403 MW; 1EFBFF42AD279FC0 CRC64;
MDGKEKKSGS KRGSKVFQFD DDADDDEPIG SLLEIMKHKS SKKDKVETES TGKQRQKQVV
EKKLSALGKD SEDMDDTLAS FRKRLKGNKK GVESGTSRVR NHEGVDTVTN SNLKPIEEAN
KNEVQSVLLR ENGASNSIQK CASETGTLLH KFSGKDKAAS PSHEKVETVS SEKEADVFHQ
ITKEESEIPM SEKAVELSRV SVPMPDVHGE VNCTIAPDKH IHLGEPTSES GYYREKNLVM
CDCGTQFNFE DRSFESNTQV TLCQKCKYSS HHNASNGGGI QVNTLEDGTA QASPVSIIPC
EDENFRGDAI SLPNSGKPST LQRPERIAKK RKLGNMVYEG DVKWENEQGF LDCQSDKSFK
GSDKCGFVPS ISKEIEIGRA AAVTAGLKAQ SVSPIEKIIL KEVLKRKGSN QEYLVCRNSI
LGLWSKNVSR ILPVTECGVT GGPSESELPS ASLIREVYKF LDQRGYINAG ISSVNGKAAS
STNQDYDLLQ GRQLEESSMA SVADSEEGVA FILGQVKAVE STSEGKKCAL QNDERDLVGC
ATSEMLESIS KKCEASIIDD NKRSVSMNAL QDSTASNVEK HPETFSVAKP ALSSTLSSAH
SNQMRGRDCV PCEVIDEKKV IVIGAGPAGL TAARHLQRQG FSVTVLEARS RVGGRVFTDR
SSLSVPVDLG ASIITGIEAD VPSERMPDPS VLVCNQLGLE LSVLHGFCPL YDTVTGKKVP
AELDDALQAE FNSLIDDVDL LVEEIGKERA NKMSLEDGLE YGLQRLRMPH DKVNIDKFGL
LNSSSKTGIR GPFMQDESWK DDFLNPLERR VMNWHFAHTE YGCAAVLKEV SLPHWNQDEF
YGGFGGPHAM IKGGYSRVVE SLAEGLDIHL NKIVSDVSYV SDVSAMDNSK HKVRVSTSNG
CEYLGDAVLV TVPLGCLKAE TIKFSPPLPD WKYASIKQLG FGVLNKVVLE FPTVFWDDSV
DYFGATAEET DLRGECFMFW NVKKTVGAPV LIALVVGKAA FEYTNKSKSE HVNHAMMVLR
KLFGGDLVPD PVASVVTDWG TDPYSYGAYS YVAIGASGED YDVLGRPVQN CLFFAGEATC
KEHPDTVGGA MMTGVREAVR IIDILRSGND YTAEIETLEK AQRKSVPVRD EVRDLIKRLE
VVELSNVLAR QSLLRNMFFS AKTTVGRLHL AKELLNLPGE TLKSFAGTKE GLAVLNSWIL
DSMGKNGTQL LRHCVHILVR VTSDLFALRL SGIGKTVKEK VCAHTSRDIR AIASQLVNVW
LDLYRKEKAN SGKKSLRQAN TTNTSRIRRK LNSPDTDSKG KLSNGNDVKT DEEFEDNQLP
MSEEEKAVFA EAEAARAAAE AAAKAFSEAY HNTSLQLPKI PSFHKFARRE QYAKMDESDF
RKKFPGNVLG RQDCMSEIDS RNCKVRDWYD FPASCLDLDS ARIPVDNYSQ PSHSNELVSH
SKFRECSGES VAADTSFLTG AWVDTGGSSD GFKDSQAIDR WQSQAAAADP EFFNRTLHIK
DEEDSIACST GPPSWKHDQR ANECSVSQVT VNKEPHKNHI RSADRLKQGV VDFVASLLMA
PYRAKKIDRD VYKSIMKKTA TKVMQHTTDV EKAMAVTQFL DSKRKNKIRD FVDKQVDKYM
VIPQVPKP
