DML3_ARATH
ID DML3_ARATH Reviewed; 1044 AA.
AC O49498; Q5XV59;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 2.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=DEMETER-like protein 3;
DE EC=3.2.2.-;
GN Name=DML3; OrderedLocusNames=At4g34060; ORFNames=F28A23.180;
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=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 [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;
RA Xiao Y.-L., Underwood B.A., Moskal W.A. Jr., Wang W., Redman J.C., Wu H.C.,
RA Utterback T., Town C.D.;
RT "Reconstruction of cDNA sequences for hypothetical genes in Arabidopsis
RT thaliana from 5' and 3' RACE products.";
RL Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NOMENCLATURE.
RX PubMed=12150995; DOI=10.1016/s0092-8674(02)00807-3;
RA Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B.,
RA Jacobsen S.E., Fischer R.L.;
RT "DEMETER, a DNA glycosylase domain protein, is required for endosperm gene
RT imprinting and seed viability in Arabidopsis.";
RL Cell 110:33-42(2002).
CC -!- FUNCTION: Potential transcriptional activator that may act by nicking
CC the target promoter. Catalyzes the release of 5-methylcytosine (5-meC)
CC from DNA by a glycosylase/lyase mechanism (By similarity).
CC {ECO:0000250}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC role in catalysis, but is probably involved in the proper positioning
CC of the enzyme along the DNA strand. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=O49498-1; Sequence=Displayed;
CC -!- DOMAIN: The DEMETER domain, which is present in proteins of the
CC subfamily, is related to the J-domain, but lacks some important
CC conserved residues.
CC -!- MISCELLANEOUS: Although strongly related to DNA glycosylase proteins,
CC it differs from these proteins. The DNA repair function may not exist.
CC -!- SIMILARITY: Belongs to the DNA glycosylase family. DEMETER subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA17566.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80123.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL021961; CAA17566.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161584; CAB80123.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86316.1; -; Genomic_DNA.
DR EMBL; AY735663; AAU44533.1; -; mRNA.
DR PIR; T05430; T05430.
DR RefSeq; NP_195132.3; NM_119567.4. [O49498-1]
DR AlphaFoldDB; O49498; -.
DR STRING; 3702.AT4G34060.1; -.
DR PaxDb; O49498; -.
DR PRIDE; O49498; -.
DR EnsemblPlants; AT4G34060.1; AT4G34060.1; AT4G34060. [O49498-1]
DR GeneID; 829552; -.
DR Gramene; AT4G34060.1; AT4G34060.1; AT4G34060. [O49498-1]
DR KEGG; ath:AT4G34060; -.
DR Araport; AT4G34060; -.
DR TAIR; locus:2124301; AT4G34060.
DR eggNOG; ENOG502QQKH; Eukaryota.
DR HOGENOM; CLU_275005_0_0_1; -.
DR InParanoid; O49498; -.
DR PhylomeDB; O49498; -.
DR PRO; PR:O49498; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O49498; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0035514; F:DNA demethylase activity; IEA:InterPro.
DR GO; GO:0019104; F:DNA N-glycosylase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IEA:InterPro.
DR GO; GO:0010216; P:maintenance of DNA methylation; IMP:TAIR.
DR Gene3D; 1.10.1670.10; -; 1.
DR InterPro; IPR044811; DME/ROS1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR028924; Perm-CXXC.
DR InterPro; IPR028925; RRM_DME.
DR PANTHER; PTHR46213; PTHR46213; 3.
DR Pfam; PF15629; Perm-CXXC; 1.
DR Pfam; PF15628; RRM_DME; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Activator; Alternative splicing; DNA-binding; Hydrolase; Iron;
KW Iron-sulfur; Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..1044
FT /note="DEMETER-like protein 3"
FT /id="PRO_0000102248"
FT REGION 1..107
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 348..445
FT /note="DEMETER"
FT REGION 1024..1044
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 14..42
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 50..71
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 72..86
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 87..102
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 678
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 685
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 688
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 694
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT CONFLICT 14
FT /note="E -> G (in Ref. 3; AAU44533)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1044 AA; 120297 MW; 1A59C80B18A2C5A8 CRC64;
MLTDGSQHTY QNGETKNSKE HERKCDESAH LQDNSQTTHK KKEKKNSKEK HGIKHSESEH
LQDDISQRVT GKGRRRNSKG TPKKLRFNRP RILEDGKKPR NPATTRLRTI SNKRRKKDID
SEDEVIPELA TPTKESFPKR RKNEKIKRSV ARTLNFKQEI VLSCLEFDKI CGPIFPRGKK
RTTTRRRYDF LCFLLPMPVW KKQSRRSKRR KNMVRWARIA SSSKLLEETL PLIVSHPTIN
GQADASLHID DTLVRHVVSK QTKKSANNVI EHLNRQITYQ KDHGLSSLAD VPLHIEDTLI
KSASSVLSER PIKKTKDIAK LIKDMGRLKI NKKVTTMIKA DKKLVTAKVN LDPETIKEWD
VLMVNDSPSR SYDDKETEAK WKKEREIFQT RIDLFINRMH RLQGNRKFKQ WKGSVVDSVV
GVFLTQNTTD YLSSNAFMSV AAKFPVDARE GLSYYIEEPQ DAKSSECIIL SDESISKVED
HENTAKRKNE KTGIIEDEIV DWNNLRRMYT KEGSRPEMHM DSVNWSDVRL SGQNVLETTI
KKRGQFRILS ERILKFLNDE VNQNGNIDLE WLRNAPSHLV KRYLLEIEGI GLKSAECVRL
LGLKHHAFPV DTNVGRIAVR LGLVPLEPLP NGVQMHQLFE YPSMDSIQKY LWPRLCKLPQ
ETLYELHYQM ITFGKVFCTK TIPNCNACPM KSECKYFASA YVSSKVLLES PEEKMHEPNT
FMNAHSQDVA VDMTSNINLV EECVSSGCSD QAICYKPLVE FPSSPRAEIP ESTDIEDVPF
MNLYQSYASV PKIDFDLDAL KKSVEDALVI SGRMSSSDEE ISKALVIPTP ENACIPIKPP
RKMKYYNRLR TEHVVYVLPD NHELLHDFER RKLDDPSPYL LAIWQPGETS SSFVPPKKKC
SSDGSKLCKI KNCSYCWTIR EQNSNIFRGT ILIPCRTAMR GAFPLNGTYF QTNEVFADHE
TSLNPIVFRR ELCKGLEKRA LYCGSTVTSI FKLLDTRRIE LCFWTGFLCL RAFDRKQRDP
KELVRRLHTP PDERGPKFMS DDDI
