DML2_ARATH
ID DML2_ARATH Reviewed; 1332 AA.
AC Q9SR66; F4J2I4;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 22-FEB-2012, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=DEMETER-like protein 2;
DE EC=3.2.2.-;
GN Name=DML2; OrderedLocusNames=At3g10010; ORFNames=T22K18.18;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 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 -!- 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 because of its large size and its unique
CC N-terminal basic domain. The DNA repair function has not been proved
CC and may not exist.
CC -!- SIMILARITY: Belongs to the DNA glycosylase family. DEMETER subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF04422.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC010927; AAF04422.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE74848.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64633.1; -; Genomic_DNA.
DR RefSeq; NP_001326647.1; NM_001337853.1.
DR RefSeq; NP_187612.5; NM_111836.5.
DR AlphaFoldDB; Q9SR66; -.
DR SMR; Q9SR66; -.
DR BioGRID; 5496; 2.
DR STRING; 3702.AT3G10010.1; -.
DR iPTMnet; Q9SR66; -.
DR PaxDb; Q9SR66; -.
DR PRIDE; Q9SR66; -.
DR ProteomicsDB; 222211; -.
DR EnsemblPlants; AT3G10010.1; AT3G10010.1; AT3G10010.
DR EnsemblPlants; AT3G10010.2; AT3G10010.2; AT3G10010.
DR GeneID; 820162; -.
DR Gramene; AT3G10010.1; AT3G10010.1; AT3G10010.
DR Gramene; AT3G10010.2; AT3G10010.2; AT3G10010.
DR KEGG; ath:AT3G10010; -.
DR Araport; AT3G10010; -.
DR TAIR; locus:2100138; AT3G10010.
DR eggNOG; ENOG502QQKH; Eukaryota.
DR HOGENOM; CLU_259012_0_0_1; -.
DR InParanoid; Q9SR66; -.
DR OMA; RSQNCEP; -.
DR OrthoDB; 164157at2759; -.
DR PRO; PR:Q9SR66; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SR66; baseline and differential.
DR Genevisible; Q9SR66; AT.
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; IEA:InterPro.
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 CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR InterPro; IPR044811; DME/ROS1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
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; 2.
DR Pfam; PF15629; Perm-CXXC; 1.
DR Pfam; PF15628; RRM_DME; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Activator; DNA-binding; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..1332
FT /note="DEMETER-like protein 2"
FT /id="PRO_0000102247"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 137..242
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 280..317
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 497..595
FT /note="DEMETER"
FT REGION 739..810
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..20
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 137..158
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 159..173
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 186..206
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 228..242
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 739..754
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 774..810
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 970
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 977
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 980
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 986
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1332 AA; 151476 MW; FB61A1C8E24B123B CRC64;
MEVEGEVREK EARVKGRQPE TEVLHGLPQE QSIFNNMQHN HQPDSDRRRL SLENLPGLYN
MSCTQLLALA NATVATGSSI GASSSSLSSQ HPTDSWINSW KMDSNPWTLS KMQKQQYDVS
TPQKFLCDLN LTPEELVSTS TQRTEPESPQ ITLKTPGKSL SETDHEPHDR IKKSVLGTGS
PAAVKKRKIA RNDEKSQLET PTLKRKKIRP KVVREGKTKK ASSKAGIKKS SIAATATKTS
EESNYVRPKR LTRRSIRFDF DLQEEDEEFC GIDFTSAGHV EGSSGEENLT DTTLGMFGHV
PKGRRGQRRS NGFKKTDNDC LSSMLSLVNT GPGSFMESEE DRPSDSQISL GRQRSIMATR
PRNFRSLKKL LQRIIPSKRD RKGCKLPRGL PKLTVASKLQ LKVFRKKRSQ RNRVASQFNA
RILDLQWRRQ NPTGTSLADI WERSLTIDAI TKLFEELDIN KEGLCLPHNR ETALILYKKS
YEEQKAIVKY SKKQKPKVQL DPETSRVWKL LMSSIDCDGV DGSDEEKRKW WEEERNMFHG
RANSFIARMR VVQGNRTFSP WKGSVVDSVV GVFLTQNVAD HSSSSAYMDL AAEFPVEWNF
NKGSCHEEWG SSVTQETILN LDPRTGVSTP RIRNPTRVII EEIDDDENDI DAVCSQESSK
TSDSSITSAD QSKTMLLDPF NTVLMNEQVD SQMVKGKGHI PYTDDLNDLS QGISMVSSAS
THCELNLNEV PPEVELCSHQ QDPESTIQTQ DQQESTRTED VKKNRKKPTT SKPKKKSKES
AKSTQKKSVD WDSLRKEAES GGRKRERTER TMDTVDWDAL RCTDVHKIAN IIIKRGMNNM
LAERIKAFLN RLVKKHGSID LEWLRDVPPD KAKEYLLSIN GLGLKSVECV RLLSLHQIAF
PVDTNVGRIA VRLGWVPLQP LPDELQMHLL ELYPVLESVQ KYLWPRLCKL DQKTLYELHY
HMITFGKVFC TKVKPNCNAC PMKAECRHYS SARASARLAL PEPEESDRTS VMIHERRSKR
KPVVVNFRPS LFLYQEKEQE AQRSQNCEPI IEEPASPEPE YIEHDIEDYP RDKNNVGTSE
DPWENKDVIP TIILNKEAGT SHDLVVNKEA GTSHDLVVLS TYAAAIPRRK LKIKEKLRTE
HHVFELPDHH SILEGFERRE AEDIVPYLLA IWTPGETVNS IQPPKQRCAL FESNNTLCNE
NKCFQCNKTR EEESQTVRGT ILIPCRTAMR GGFPLNGTYF QTNEVFADHD SSINPIDVPT
ELIWDLKRRV AYLGSSVSSI CKGLSVEAIK YNFQEGYVCV RGFDRENRKP KSLVKRLHCS
HVAIRTKEKT EE
