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   10-MAY-2017, entry version 85.
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; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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.,
RA   Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
RA   Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
RA   De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
RA   Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
RA   Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
RA   Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
RA   Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
RA   Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
RA   Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
RA   Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
RA   Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
RA   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.,
RA   Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
RA   Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
RA   Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
RA   Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
RA   Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
RA   Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
RA   Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
RA   Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
RA   Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
RA   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
RT   thaliana.";
RL   Nature 408:820-822(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Portal (Araport);
RL   Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
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.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., 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,
RP   MUTAGENESIS 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
RT   nuclear DNA glycosylase MBD4L in Arabidopsis.";
RL   Plant Sci. 235:122-129(2015).
CC   -!- FUNCTION: Monofunctional DNA glycosylase targeting U:G and T:G
CC       mispairs (PubMed:23994068). Excises uracil derivatives and
CC       exhibits a preference for a CpG sequence context, irrespective of
CC       the methylation status of the complementary strand
CC       (PubMed:23994068). The activity follows a biphasic kinetics, with
CC       an initial burst of product accumulation followed by a slower
CC       phase (PubMed:23994068). Specifically binds its reaction product
CC       (PubMed:23994068). Triggers the base excision repair (BER) pathway
CC       (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         Note=No experimental confirmation available. Derived from EST
CC         data. {ECO:0000305};
CC       Name=3;
CC         IsoId=Q0IGK1-3; Sequence=VSP_057787, VSP_057789;
CC         Note=No experimental confirmation available. {ECO:0000305};
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         Note=No experimental confirmation available. {ECO:0000305};
CC   -!- TISSUE SPECIFICITY: Isoform 1 and isoform 4: Expressed in leaves
CC       and flowers, but not in roots or stems.
CC       {ECO:0000269|PubMed:25900572}.
CC   -!- DOMAIN: The N-terminal domain (1-290) does not play any direct
CC       role in catalysis and is not required for product binding.
CC       {ECO:0000269|PubMed:23994068}.
CC   -!- CAUTION: This putative homolog of vertebrate MBD4 DNA glycosylase
CC       is designated as MBD4L (MBD4-like) to avoid nomenclature confusion
CC       with a protein with a conserved MBD but no DNA glycosylase domain
CC       already called MBD4 (AC Q9LYB9). {ECO:0000303|PubMed:23994068}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF21203.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
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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   UniGene; At.40281; -.
DR   ProteinModelPortal; Q0IGK1; -.
DR   SMR; Q0IGK1; -.
DR   PaxDb; Q0IGK1; -.
DR   EnsemblPlants; AT3G07930.3; AT3G07930.3; AT3G07930. [Q0IGK1-1]
DR   GeneID; 819984; -.
DR   Gramene; AT3G07930.3; AT3G07930.3; AT3G07930.
DR   KEGG; ath:AT3G07930; -.
DR   Araport; AT3G07930; -.
DR   TAIR; locus:2077357; AT3G07930.
DR   eggNOG; ENOG410IXQY; Eukaryota.
DR   eggNOG; ENOG4111HPQ; LUCA.
DR   HOGENOM; HOG000119219; -.
DR   InParanoid; Q0IGK1; -.
DR   KO; K10801; -.
DR   OMA; WHDPWRV; -.
DR   OrthoDB; EOG09360D9M; -.
DR   PhylomeDB; Q0IGK1; -.
DR   Reactome; R-ATH-110329; Cleavage of the damaged pyrimidine.
DR   Reactome; R-ATH-110357; Displacement of DNA glycosylase by APEX1.
DR   PRO; PR:Q0IGK1; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   Genevisible; Q0IGK1; AT.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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   SUPFAM; SSF48150; SSF48150; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Complete proteome; DNA damage; DNA repair;
KW   Hydrolase; Nucleus; Reference proteome.
FT   CHAIN         1    445       Methyl-CpG-binding domain protein 4-like
FT                                protein.
FT                                /FTId=PRO_0000433478.
FT   COMPBIAS    123    127       Poly-Asp. {ECO:0000255}.
FT   ACT_SITE    429    429       {ECO:0000250}.
FT   VAR_SEQ      39    154       Missing (in isoform 4).
FT                                /FTId=VSP_057785.
FT   VAR_SEQ     139    176       Missing (in isoform 5).
FT                                /FTId=VSP_057786.
FT   VAR_SEQ     340    352       GAQTRGVISDLFG -> DAGSDIRLVWIVY (in
FT                                isoform 3).
FT                                /FTId=VSP_057787.
FT   VAR_SEQ     343    358       TRGVISDLFGLCTDAK -> VIADAGSDIRLVWIVY (in
FT                                isoform 2).
FT                                /FTId=VSP_057788.
FT   VAR_SEQ     353    445       Missing (in isoform 3).
FT                                /FTId=VSP_057789.
FT   VAR_SEQ     359    445       Missing (in isoform 2).
FT                                /FTId=VSP_057790.
FT   MUTAGEN     429    429       D->A: Reduces activity 160-fold.
FT                                {ECO:0000269|PubMed:23994068}.
FT   CONFLICT    139    139       C -> W (in Ref. 5; AAM64924).
FT                                {ECO:0000305}.
FT   CONFLICT    224    224       V -> A (in Ref. 3; AAO22623).
FT                                {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
//