MBD4L_ARATH
ID MBD4L_ARATH Reviewed; 445 AA.
AC Q0IGK1; F4JFQ3; Q3EBA6; Q84WT3; Q8LB76; Q9SFC1;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Methyl-CpG-binding domain protein 4-like protein {ECO:0000303|PubMed:23994068};
DE EC=3.2.2.- {ECO:0000305};
DE AltName: Full=Protein MBD4-like {ECO:0000303|PubMed:23994068};
GN Name=MBD4L {ECO:0000303|PubMed:23994068};
GN OrderedLocusNames=At3g07930 {ECO:0000312|Araport:AT3G07930};
GN ORFNames=F17A17.27 {ECO:0000312|EMBL:AAF21203.1};
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 {ECO:0000312|EMBL:ABI49466.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF Clones.";
RL Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP IDENTIFICATION, NOMENCLATURE, 3D-STRUCTURE MODELING, FUNCTION, MUTAGENESIS
RP OF ASP-429, AND DOMAIN.
RX PubMed=23994068; DOI=10.1016/j.dnarep.2013.08.002;
RA Ramiro-Merina A., Ariza R.R., Roldan-Arjona T.;
RT "Molecular characterization of a putative plant homolog of MBD4 DNA
RT glycosylase.";
RL DNA Repair 12:890-898(2013).
RN [7]
RP FUNCTION, ALTERNATIVE SPLICING (ISOFORMS 1 AND 4), TISSUE SPECIFICITY
RP (ISOFORMS 1 AND 4), AND SUBCELLULAR LOCATION.
RX PubMed=25900572; DOI=10.1016/j.plantsci.2015.03.011;
RA Nota F., Cambiagno D.A., Ribone P., Alvarez M.E.;
RT "Expression and function of AtMBD4L, the single gene encoding the nuclear
RT DNA glycosylase MBD4L in Arabidopsis.";
RL Plant Sci. 235:122-129(2015).
CC -!- FUNCTION: Monofunctional DNA glycosylase targeting U:G and T:G mispairs
CC (PubMed:23994068). Excises uracil derivatives and exhibits a preference
CC for a CpG sequence context, irrespective of the methylation status of
CC the complementary strand (PubMed:23994068). The activity follows a
CC biphasic kinetics, with an initial burst of product accumulation
CC followed by a slower phase (PubMed:23994068). Specifically binds its
CC reaction product (PubMed:23994068). Triggers the base excision repair
CC (BER) pathway (PubMed:25900572). {ECO:0000269|PubMed:23994068,
CC ECO:0000269|PubMed:25900572}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25900572}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1; Synonyms=MBD4L3 {ECO:0000303|PubMed:25900572};
CC IsoId=Q0IGK1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q0IGK1-2; Sequence=VSP_057788, VSP_057790;
CC Name=3;
CC IsoId=Q0IGK1-3; Sequence=VSP_057787, VSP_057789;
CC Name=4; Synonyms=MBD4L4 {ECO:0000303|PubMed:25900572};
CC IsoId=Q0IGK1-4; Sequence=VSP_057785;
CC Name=5;
CC IsoId=Q0IGK1-5; Sequence=VSP_057786;
CC -!- TISSUE SPECIFICITY: Isoform 1 and isoform 4: Expressed in leaves and
CC flowers, but not in roots or stems. {ECO:0000269|PubMed:25900572}.
CC -!- DOMAIN: The N-terminal domain (1-290) does not play any direct role in
CC catalysis and is not required for product binding.
CC {ECO:0000269|PubMed:23994068}.
CC -!- CAUTION: This putative homolog of vertebrate MBD4 DNA glycosylase is
CC designated as MBD4L (MBD4-like) to avoid nomenclature confusion with a
CC protein with a conserved MBD but no DNA glycosylase domain already
CC called MBD4 (AC Q9LYB9). {ECO:0000303|PubMed:23994068}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF21203.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC013483; AAF21203.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002686; AEE74620.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74621.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74622.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65422.1; -; Genomic_DNA.
DR EMBL; BT002799; AAO22623.1; -; mRNA.
DR EMBL; BT028919; ABI49466.1; -; mRNA.
DR EMBL; AY087374; AAM64924.1; -; mRNA.
DR RefSeq; NP_001327391.1; NM_001337751.1. [Q0IGK1-4]
DR RefSeq; NP_566325.1; NM_111672.3. [Q0IGK1-3]
DR RefSeq; NP_974252.1; NM_202523.1. [Q0IGK1-2]
DR RefSeq; NP_974253.1; NM_202524.2. [Q0IGK1-1]
DR AlphaFoldDB; Q0IGK1; -.
DR SMR; Q0IGK1; -.
DR STRING; 3702.AT3G07930.3; -.
DR PaxDb; Q0IGK1; -.
DR PRIDE; Q0IGK1; -.
DR EnsemblPlants; AT3G07930.1; AT3G07930.1; AT3G07930. [Q0IGK1-3]
DR EnsemblPlants; AT3G07930.2; AT3G07930.2; AT3G07930. [Q0IGK1-2]
DR EnsemblPlants; AT3G07930.3; AT3G07930.3; AT3G07930. [Q0IGK1-1]
DR EnsemblPlants; AT3G07930.4; AT3G07930.4; AT3G07930. [Q0IGK1-4]
DR GeneID; 819984; -.
DR Gramene; AT3G07930.1; AT3G07930.1; AT3G07930. [Q0IGK1-3]
DR Gramene; AT3G07930.2; AT3G07930.2; AT3G07930. [Q0IGK1-2]
DR Gramene; AT3G07930.3; AT3G07930.3; AT3G07930. [Q0IGK1-1]
DR Gramene; AT3G07930.4; AT3G07930.4; AT3G07930. [Q0IGK1-4]
DR KEGG; ath:AT3G07930; -.
DR Araport; AT3G07930; -.
DR TAIR; locus:2077357; AT3G07930.
DR eggNOG; ENOG502RY32; Eukaryota.
DR HOGENOM; CLU_051571_0_0_1; -.
DR InParanoid; Q0IGK1; -.
DR OMA; PSSECDG; -.
DR OrthoDB; 1574293at2759; -.
DR PhylomeDB; Q0IGK1; -.
DR PRO; PR:Q0IGK1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q0IGK1; baseline and differential.
DR Genevisible; Q0IGK1; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR045138; MeCP2/MBD4.
DR PANTHER; PTHR15074; PTHR15074; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; Hydrolase; Nucleus;
KW Reference proteome.
FT CHAIN 1..445
FT /note="Methyl-CpG-binding domain protein 4-like protein"
FT /id="PRO_0000433478"
FT ACT_SITE 429
FT /evidence="ECO:0000250"
FT VAR_SEQ 39..154
FT /note="Missing (in isoform 4)"
FT /id="VSP_057785"
FT VAR_SEQ 139..176
FT /note="Missing (in isoform 5)"
FT /id="VSP_057786"
FT VAR_SEQ 340..352
FT /note="GAQTRGVISDLFG -> DAGSDIRLVWIVY (in isoform 3)"
FT /id="VSP_057787"
FT VAR_SEQ 343..358
FT /note="TRGVISDLFGLCTDAK -> VIADAGSDIRLVWIVY (in isoform 2)"
FT /id="VSP_057788"
FT VAR_SEQ 353..445
FT /note="Missing (in isoform 3)"
FT /id="VSP_057789"
FT VAR_SEQ 359..445
FT /note="Missing (in isoform 2)"
FT /id="VSP_057790"
FT MUTAGEN 429
FT /note="D->A: Reduces activity 160-fold."
FT /evidence="ECO:0000269|PubMed:23994068"
FT CONFLICT 139
FT /note="C -> W (in Ref. 5; AAM64924)"
FT /evidence="ECO:0000305"
FT CONFLICT 224
FT /note="V -> A (in Ref. 3; AAO22623)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 445 AA; 51135 MW; CE797C539BED410D CRC64;
MVPPIIYKYK RRKDRRLGRD DDSSVMMTRR RPDSDFIEVS DENRSFALFK EDDEKNRDLG
LVDDGSTNLV LQCHDDGCSL EKDNSNSLDD LFSGFVYKGV RRRKRDDFGS ITTSNLVSPQ
IADDDDDSVS DSHIERQECS EFHVEVRRVS PYFQGSTVSQ QSKEGCDSDS VCSKEGCSKV
QAKVPRVSPY FQASTISQCD SDIVSSSQSG RNYRKGSSKR QVKVRRVSPY FQESTVSEQP
NQAPKGLRNY FKVVKVSRYF HADGIQVNES QKEKSRNVRK TPIVSPVLSL SQKTDDVYLR
KTPDNTWVPP RSPCNLLQED HWHDPWRVLV ICMLLNKTSG AQTRGVISDL FGLCTDAKTA
TEVKEEEIEN LIKPLGLQKK RTKMIQRLSL EYLQESWTHV TQLHGVGKYA ADAYAIFCNG
NWDRVKPNDH MLNYYWDYLR IRYKL
