ID MBD4_HUMAN Reviewed; 580 AA.
AC O95243; B4DZN2; D3DNC3; D3DNC4; E9PEE4; Q2MD36; Q7Z4T3; Q96F09;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 27-MAR-2024, entry version 184.
DE RecName: Full=Methyl-CpG-binding domain protein 4;
DE EC=3.2.2.-;
DE AltName: Full=Methyl-CpG-binding endonuclease 1;
DE AltName: Full=Methyl-CpG-binding protein MBD4;
DE AltName: Full=Mismatch-specific DNA N-glycosylase;
GN Name=MBD4 {ECO:0000312|HGNC:HGNC:6919};
GN Synonyms=MED1 {ECO:0000305|PubMed:9774669};
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=9774669; DOI=10.1128/mcb.18.11.6538;
RA Hendrich B., Bird A.;
RT "Identification and characterization of a family of mammalian methyl-CpG
RT binding proteins.";
RL Mol. Cell. Biol. 18:6538-6547(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=10441743; DOI=10.1007/s003359901112;
RA Hendrich B., Abbott C., McQueen H., Chambers D., Cross S.H., Bird A.;
RT "Genomic structure and chromosomal mapping of the murine and human mbd1,
RT mbd2, mbd3, and mbd4 genes.";
RL Mamm. Genome 10:906-912(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND INTERACTION WITH
RP MLH1.
RC TISSUE=Fetal brain;
RX PubMed=10097147; DOI=10.1073/pnas.96.7.3969;
RA Bellacosa A., Cicchillitti L., Schepis F., Riccio A., Yeung A.T.,
RA Matsumoto Y., Golemis E.A., Genuardi M., Neri G.;
RT "MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA
RT mismatch repair protein MLH1.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:3969-3974(1999).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4), AND ALTERNATIVE SPLICING.
RX PubMed=17143486;
RA Owen R.M., Baker R.D., Bader S., Dunlop M.G., Nicholl I.D.;
RT "The identification of a novel alternatively spliced form of the MBD4 DNA
RT glycosylase.";
RL Oncol. Rep. 17:111-116(2007).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC TISSUE=Lung;
RA Guo J.H., Chen L., Yu L.;
RL Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5).
RC TISSUE=Testis;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RA Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
RT "Cloning of human full open reading frames in Gateway(TM) system entry
RT vector (pDONR201).";
RL Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS SER-273; PRO-342; LYS-346
RP AND HIS-568.
RG NIEHS SNPs program;
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16641997; DOI=10.1038/nature04728;
RA Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J.,
RA Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P.,
RA Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A.,
RA Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L.,
RA Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G.,
RA Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W.,
RA Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M.,
RA Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P.,
RA Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H.,
RA Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J.,
RA Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W.,
RA Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B.,
RA Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O.,
RA Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B.,
RA Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H.,
RA Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J.,
RA Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X.,
RA Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R.,
RA Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.;
RT "The DNA sequence, annotation and analysis of human chromosome 3.";
RL Nature 440:1194-1198(2006).
RN [10]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [11]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Lung;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [12]
RP FUNCTION.
RX PubMed=10930409; DOI=10.1074/jbc.m004535200;
RA Petronzelli F., Riccio A., Markham G.D., Seeholzer S.H., Stoerker J.,
RA Genuardi M., Yeung A.T., Matsumoto Y., Bellacosa A.;
RT "Biphasic kinetics of the human DNA repair protein MED1 (MBD4), a mismatch-
RT specific DNA N-glycosylase.";
RL J. Biol. Chem. 275:32422-32429(2000).
RN [13]
RP INTERACTION WITH FADD.
RX PubMed=12702765; DOI=10.1073/pnas.0431215100;
RA Screaton R.A., Kiessling S., Sansom O.J., Millar C.B., Maddison K.,
RA Bird A., Clarke A.R., Frisch S.M.;
RT "Fas-associated death domain protein interacts with methyl-CpG binding
RT domain protein 4: a potential link between genome surveillance and
RT apoptosis.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:5211-5216(2003).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-318 AND SER-428, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [16]
RP VARIANTS TPDS2 255-SER--SER-580 DEL; 431-ARG--SER-580 DEL; 546-ARG--SER-580
RP DEL; 563-LEU--SER-580 DEL AND HIS-567 DEL, INVOLVEMENT IN TPDS2,
RP CHARACTERIZATION OF VARIANT TPDS2 HIS-567 DEL, AND MUTAGENESIS OF ASP-560.
RX PubMed=30049810; DOI=10.1182/blood-2018-05-852566;
RA Sanders M.A., Chew E., Flensburg C., Zeilemaker A., Miller S.E.,
RA Al Hinai A.S., Bajel A., Luiken B., Rijken M., Mclennan T.,
RA Hoogenboezem R.M., Kavelaars F.G., Froehling S., Blewitt M.E.,
RA Bindels E.M., Alexander W.S., Loewenberg B., Roberts A.W., Valk P.J.M.,
RA Majewski I.J.;
RT "MBD4 guards against methylation damage and germ line deficiency
RT predisposes to clonal hematopoiesis and early-onset AML.";
RL Blood 132:1526-1534(2018).
RN [17]
RP VARIANT UVM1 563-LEU--SER-580 DEL, AND INVOLVEMENT IN UVM1.
RX PubMed=30714079; DOI=10.1007/s00251-019-01108-x;
RA Johansson P.A., Stark A., Palmer J.M., Bigby K., Brooks K., Rolfe O.,
RA Pritchard A.L., Whitehead K., Warrier S., Glasson W., Hayward N.K.;
RT "Prolonged stable disease in a uveal melanoma patient with germline MBD4
RT nonsense mutation treated with pembrolizumab and ipilimumab.";
RL Immunogenetics 71:433-436(2019).
RN [18]
RP ERRATUM OF PUBMED:30714079.
RX PubMed=31147739; DOI=10.1007/s00251-019-01120-1;
RA Johansson P.A., Stark A., Palmer J.M., Bigby K., Brooks K., Rolfe O.,
RA Pritchard A.L., Whitehead K., Warrier S., Glasson W., Hayward N.K.;
RL Immunogenetics 71:511-511(2019).
RN [19]
RP VARIANT TPDS2 73-GLN--SER-580 DEL, AND CHARACTERIZATION OF VARIANT TPDS2
RP 73-GLN--SER-580 DEL.
RX PubMed=31322271; DOI=10.3892/or.2019.7239;
RA Tanakaya K., Kumamoto K., Tada Y., Eguchi H., Ishibashi K., Idani H.,
RA Tachikawa T., Akagi K., Okazaki Y., Ishida H.;
RT "A germline MBD4 mutation was identified in a patient with colorectal
RT oligopolyposis and early-onset cancer: A case report.";
RL Oncol. Rep. 42:1133-1140(2019).
RN [20]
RP VARIANTS UVM1 181-ARG--SER-580 DEL; TRP-468 AND 569-TRP--SER-580 DEL,
RP INVOLVEMENT IN UVM1, AND CHARACTERIZATION OF VARIANTS UVM1 TRP-468 AND
RP 569-TRP--SER-580 DEL.
RX PubMed=32239153; DOI=10.1093/jnci/djaa047;
RA Derrien A.C., Rodrigues M., Eeckhoutte A., Dayot S., Houy A., Mobuchon L.,
RA Gardrat S., Lequin D., Ballet S., Pierron G., Alsafadi S., Mariani O.,
RA El-Marjou A., Matet A., Colas C., Cassoux N., Stern M.H.;
RT "Germline MBD4 Mutations and Predisposition to Uveal Melanoma.";
RL J. Natl. Cancer Inst. 113:80-87(2021).
RN [21]
RP VARIANT TPDS2 563-LEU--SER-580 DEL, AND INVOLVEMENT IN TPDS2.
RX PubMed=35460607; DOI=10.1016/j.ajhg.2022.03.018;
RG Genomics England Research Consortium;
RG CORGI Consortium;
RG WGS500 Consortium;
RA Palles C., West H.D., Chew E., Galavotti S., Flensburg C., Grolleman J.E.,
RA Jansen E.A.M., Curley H., Chegwidden L., Arbe-Barnes E.H., Lander N.,
RA Truscott R., Pagan J., Bajel A., Sherwood K., Martin L., Thomas H.,
RA Georgiou D., Fostira F., Goldberg Y., Adams D.J., van der Biezen S.A.M.,
RA Christie M., Clendenning M., Thomas L.E., Deltas C., Dimovski A.J.,
RA Dymerska D., Lubinski J., Mahmood K., van der Post R.S., Sanders M.,
RA Weitz J., Taylor J.C., Turnbull C., Vreede L., van Wezel T., Whalley C.,
RA Arnedo-Pac C., Caravagna G., Cross W., Chubb D., Frangou A., Gruber A.J.,
RA Kinnersley B., Noyvert B., Church D., Graham T., Houlston R.,
RA Lopez-Bigas N., Sottoriva A., Wedge D., Jenkins M.A., Kuiper R.P.,
RA Roberts A.W., Cheadle J.P., Ligtenberg M.J.L., Hoogerbrugge N.,
RA Koelzer V.H., Rivas A.D., Winship I.M., Ponte C.R., Buchanan D.D.,
RA Power D.G., Green A., Tomlinson I.P.M., Sampson J.R., Majewski I.J.,
RA de Voer R.M.;
RT "Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.";
RL Am. J. Hum. Genet. 109:953-960(2022).
CC -!- FUNCTION: Mismatch-specific DNA N-glycosylase involved in DNA repair.
CC Has thymine glycosylase activity and is specific for G:T mismatches
CC within methylated and unmethylated CpG sites. Can also remove uracil or
CC 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first
CC identified as methyl-CpG-binding protein. {ECO:0000269|PubMed:10097147,
CC ECO:0000269|PubMed:10930409}.
CC -!- SUBUNIT: Interacts with MLH1. {ECO:0000269|PubMed:10097147,
CC ECO:0000269|PubMed:12702765}.
CC -!- INTERACTION:
CC O95243; Q13158: FADD; NbExp=6; IntAct=EBI-348011, EBI-494804;
CC O95243-2; P28799: GRN; NbExp=3; IntAct=EBI-6448717, EBI-747754;
CC O95243-2; P42858: HTT; NbExp=19; IntAct=EBI-6448717, EBI-466029;
CC O95243-2; P40692: MLH1; NbExp=3; IntAct=EBI-6448717, EBI-744248;
CC O95243-2; P11245: NAT2; NbExp=3; IntAct=EBI-6448717, EBI-9057228;
CC O95243-2; O76024: WFS1; NbExp=3; IntAct=EBI-6448717, EBI-720609;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1;
CC IsoId=O95243-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O95243-2; Sequence=VSP_010816;
CC Name=3;
CC IsoId=O95243-3; Sequence=VSP_010817, VSP_010818;
CC Name=5;
CC IsoId=O95243-5; Sequence=VSP_054846;
CC Name=4;
CC IsoId=O95243-6; Sequence=VSP_054845;
CC -!- DISEASE: Tumor predisposition syndrome 2 (TPDS2) [MIM:619975]: An
CC autosomal recessive condition characterized by predisposition to
CC develop a variety of tumors or malignancies, including acute myeloid
CC leukemia, myelodysplastic syndrome, colorectal adenomatous polyposis
CC and carcinoma, and uveal melanoma. {ECO:0000269|PubMed:30049810,
CC ECO:0000269|PubMed:31322271, ECO:0000269|PubMed:35460607}. Note=The
CC disease is caused by variants affecting the gene represented in this
CC entry.
CC -!- DISEASE: Melanoma, uveal, 1 (UVM1) [MIM:606660]: Most common
CC intraocular malignancy, arising from melanocytes in the iris, ciliary
CC body, or choroid. Metastases develop in more than 30% of case patients,
CC almost invariably in the liver, with poor prognosis.
CC {ECO:0000269|PubMed:30714079, ECO:0000269|PubMed:32239153}.
CC Note=Disease susceptibility is associated with variants affecting the
CC gene represented in this entry.
CC -!- MISCELLANEOUS: [Isoform 4]: Possesses uracil DNA glycosylase but not
CC thymine DNA glycosylase activity. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=NIEHS-SNPs;
CC URL="http://egp.gs.washington.edu/data/mbd4/";
CC -!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and
CC Haematology;
CC URL="https://atlasgeneticsoncology.org/gene/41312/MBD4";
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DR EMBL; AF072250; AAC68879.1; -; mRNA.
DR EMBL; AF120999; AAD50374.1; -; Genomic_DNA.
DR EMBL; AF120997; AAD50374.1; JOINED; Genomic_DNA.
DR EMBL; AF120998; AAD50374.1; JOINED; Genomic_DNA.
DR EMBL; AF114784; AAD22195.1; -; mRNA.
DR EMBL; AM180876; CAJ55826.1; -; mRNA.
DR EMBL; AF532602; AAP97338.1; -; mRNA.
DR EMBL; AK303013; BAG64144.1; -; mRNA.
DR EMBL; CR450305; CAG29301.1; -; mRNA.
DR EMBL; AF494057; AAM00008.1; -; Genomic_DNA.
DR EMBL; AL449212; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471052; EAW79251.1; -; Genomic_DNA.
DR EMBL; CH471052; EAW79253.1; -; Genomic_DNA.
DR EMBL; CH471052; EAW79254.1; -; Genomic_DNA.
DR EMBL; CH471052; EAW79255.1; -; Genomic_DNA.
DR EMBL; BC011752; AAH11752.1; -; mRNA.
DR CCDS; CCDS3058.1; -. [O95243-1]
DR CCDS; CCDS63766.1; -. [O95243-5]
DR CCDS; CCDS63767.1; -. [O95243-3]
DR CCDS; CCDS63768.1; -. [O95243-2]
DR CCDS; CCDS63769.1; -. [O95243-6]
DR RefSeq; NP_001263199.1; NM_001276270.1. [O95243-2]
DR RefSeq; NP_001263200.1; NM_001276271.1. [O95243-5]
DR RefSeq; NP_001263201.1; NM_001276272.1. [O95243-3]
DR RefSeq; NP_001263202.1; NM_001276273.1. [O95243-6]
DR RefSeq; NP_003916.1; NM_003925.2. [O95243-1]
DR PDB; 2MOE; NMR; -; A=80-148.
DR PDB; 3IHO; X-ray; 2.70 A; A=437-574.
DR PDB; 4DK9; X-ray; 2.76 A; A=426-580.
DR PDB; 4E9E; X-ray; 1.90 A; A=427-580.
DR PDB; 4E9F; X-ray; 1.79 A; A=427-580.
DR PDB; 4E9G; X-ray; 2.35 A; A=427-580.
DR PDB; 4E9H; X-ray; 3.00 A; A=427-580.
DR PDB; 4EA4; X-ray; 2.00 A; A=427-574.
DR PDB; 4EA5; X-ray; 2.14 A; A=427-580.
DR PDB; 4LG7; X-ray; 2.50 A; A=83-149.
DR PDB; 4OFA; X-ray; 1.55 A; A=426-580.
DR PDB; 4OFE; X-ray; 2.15 A; A=426-580.
DR PDB; 4OFH; X-ray; 2.22 A; A=426-580.
DR PDB; 5CHZ; X-ray; 1.83 A; A=426-580.
DR PDB; 6VJW; X-ray; 2.02 A; A=438-575.
DR PDB; 7KZ0; X-ray; 1.57 A; A=426-580.
DR PDB; 7KZ1; X-ray; 1.62 A; A=426-580.
DR PDB; 7KZG; X-ray; 1.68 A; A=426-580.
DR PDBsum; 2MOE; -.
DR PDBsum; 3IHO; -.
DR PDBsum; 4DK9; -.
DR PDBsum; 4E9E; -.
DR PDBsum; 4E9F; -.
DR PDBsum; 4E9G; -.
DR PDBsum; 4E9H; -.
DR PDBsum; 4EA4; -.
DR PDBsum; 4EA5; -.
DR PDBsum; 4LG7; -.
DR PDBsum; 4OFA; -.
DR PDBsum; 4OFE; -.
DR PDBsum; 4OFH; -.
DR PDBsum; 5CHZ; -.
DR PDBsum; 6VJW; -.
DR PDBsum; 7KZ0; -.
DR PDBsum; 7KZ1; -.
DR PDBsum; 7KZG; -.
DR AlphaFoldDB; O95243; -.
DR BMRB; O95243; -.
DR SMR; O95243; -.
DR BioGRID; 114444; 87.
DR IntAct; O95243; 26.
DR MINT; O95243; -.
DR STRING; 9606.ENSP00000249910; -.
DR GlyGen; O95243; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; O95243; -.
DR MetOSite; O95243; -.
DR PhosphoSitePlus; O95243; -.
DR BioMuta; MBD4; -.
DR EPD; O95243; -.
DR jPOST; O95243; -.
DR MassIVE; O95243; -.
DR MaxQB; O95243; -.
DR PaxDb; 9606-ENSP00000249910; -.
DR PeptideAtlas; O95243; -.
DR ProteomicsDB; 19871; -.
DR ProteomicsDB; 50740; -. [O95243-1]
DR ProteomicsDB; 50741; -. [O95243-2]
DR ProteomicsDB; 50742; -. [O95243-3]
DR ProteomicsDB; 61389; -.
DR Pumba; O95243; -.
DR TopDownProteomics; O95243-3; -. [O95243-3]
DR ABCD; O95243; 2 sequenced antibodies.
DR Antibodypedia; 1087; 252 antibodies from 33 providers.
DR DNASU; 8930; -.
DR Ensembl; ENST00000249910.5; ENSP00000249910.1; ENSG00000129071.10. [O95243-1]
DR Ensembl; ENST00000393278.6; ENSP00000376959.2; ENSG00000129071.10. [O95243-6]
DR Ensembl; ENST00000429544.7; ENSP00000394080.2; ENSG00000129071.10. [O95243-2]
DR Ensembl; ENST00000503197.5; ENSP00000424873.1; ENSG00000129071.10. [O95243-3]
DR Ensembl; ENST00000507208.1; ENSP00000422327.1; ENSG00000129071.10. [O95243-5]
DR GeneID; 8930; -.
DR KEGG; hsa:8930; -.
DR MANE-Select; ENST00000429544.7; ENSP00000394080.2; NM_001276270.2; NP_001263199.1. [O95243-2]
DR UCSC; uc003emh.3; human. [O95243-1]
DR AGR; HGNC:6919; -.
DR CTD; 8930; -.
DR DisGeNET; 8930; -.
DR GeneCards; MBD4; -.
DR HGNC; HGNC:6919; MBD4.
DR HPA; ENSG00000129071; Low tissue specificity.
DR MalaCards; MBD4; -.
DR MIM; 603574; gene.
DR MIM; 606660; phenotype.
DR MIM; 619975; phenotype.
DR neXtProt; NX_O95243; -.
DR OpenTargets; ENSG00000129071; -.
DR PharmGKB; PA30663; -.
DR VEuPathDB; HostDB:ENSG00000129071; -.
DR eggNOG; KOG4161; Eukaryota.
DR GeneTree; ENSGT00530000063687; -.
DR HOGENOM; CLU_034167_0_0_1; -.
DR InParanoid; O95243; -.
DR OMA; MTECHKS; -.
DR OrthoDB; 1451962at2759; -.
DR PhylomeDB; O95243; -.
DR TreeFam; TF329176; -.
DR PathwayCommons; O95243; -.
DR Reactome; R-HSA-110328; Recognition and association of DNA glycosylase with site containing an affected pyrimidine.
DR Reactome; R-HSA-110329; Cleavage of the damaged pyrimidine.
DR Reactome; R-HSA-110357; Displacement of DNA glycosylase by APEX1.
DR SignaLink; O95243; -.
DR BioGRID-ORCS; 8930; 7 hits in 1180 CRISPR screens.
DR ChiTaRS; MBD4; human.
DR EvolutionaryTrace; O95243; -.
DR GeneWiki; MBD4; -.
DR GenomeRNAi; 8930; -.
DR Pharos; O95243; Tbio.
DR PRO; PR:O95243; -.
DR Proteomes; UP000005640; Chromosome 3.
DR RNAct; O95243; Protein.
DR Bgee; ENSG00000129071; Expressed in secondary oocyte and 215 other cell types or tissues.
DR ExpressionAtlas; O95243; baseline and differential.
DR Genevisible; O95243; HS.
DR GO; GO:0016607; C:nuclear speck; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0004520; F:DNA endonuclease activity; TAS:ProtInc.
DR GO; GO:0019104; F:DNA N-glycosylase activity; TAS:Reactome.
DR GO; GO:0008263; F:pyrimidine-specific mismatch base pair DNA N-glycosylase activity; IDA:MGI.
DR GO; GO:0003696; F:satellite DNA binding; TAS:ProtInc.
DR GO; GO:0045008; P:depyrimidination; TAS:Reactome.
DR GO; GO:0006281; P:DNA repair; TAS:ProtInc.
DR GO; GO:0032355; P:response to estradiol; IEA:Ensembl.
DR CDD; cd01396; MeCP2_MBD; 1.
DR IDEAL; IID00696; -.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR017352; MBD4.
DR InterPro; IPR045138; MeCP2/MBD4.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR PANTHER; PTHR15074:SF7; METHYL-CPG-BINDING DOMAIN PROTEIN 4; 1.
DR PANTHER; PTHR15074; METHYL-CPG-BINDING PROTEIN; 1.
DR Pfam; PF01429; MBD; 1.
DR PIRSF; PIRSF038005; Methyl_CpG_bd_MBD4; 1.
DR SMART; SM00391; MBD; 1.
DR SUPFAM; SSF54171; DNA-binding domain; 1.
DR SUPFAM; SSF48150; DNA-glycosylase; 1.
DR PROSITE; PS50982; MBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Disease variant; DNA damage;
KW DNA repair; DNA-binding; Hydrolase; Nucleus; Phosphoprotein;
KW Reference proteome.
FT CHAIN 1..580
FT /note="Methyl-CpG-binding domain protein 4"
FT /id="PRO_0000096264"
FT DOMAIN 76..148
FT /note="MBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT REGION 1..36
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 560
FT /evidence="ECO:0000250"
FT MOD_RES 318
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 428
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT VAR_SEQ 83..401
FT /note="RKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGET
FT SLKPEDFDFTVLSKRGIKSRYKDCSMAALTSHLQNQSNNSNWNLRTRSKCKKDVFMPPS
FT SSSELQESRGLSNFTSTHLLLKEDEGVDDVNFRKVRKPKGKVTILKGIPIKKTKKGCRK
FT SCSGFVQSDSKRESVCNKADAESEPVAQKSQLDRTVCISDAGACGETLSVTSEENSLVK
FT KKERSLSSGSNFCSEQKTSGIINKFCSAKDSEHNEKYEDTFLESEEIGTKVEVVERKEH
FT LHTDILKRGSEMDNNCSPTRKDFTGEKIFQE -> Q (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:17143486"
FT /id="VSP_054845"
FT VAR_SEQ 395..400
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334, ECO:0000303|Ref.7"
FT /id="VSP_010816"
FT VAR_SEQ 539..540
FT /note="KY -> AP (in isoform 3)"
FT /evidence="ECO:0000303|Ref.5"
FT /id="VSP_010817"
FT VAR_SEQ 541..580
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|Ref.5"
FT /id="VSP_010818"
FT VAR_SEQ 557..580
FT /note="HPEDHKLNKYHDWLWENHEKLSLS -> RLTPIHNSAHLVSEAK (in
FT isoform 5)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_054846"
FT VARIANT 61
FT /note="C -> R (in dbSNP:rs2307296)"
FT /id="VAR_029306"
FT VARIANT 73..580
FT /note="Missing (in TPDS2; no MBD4 protein detected by
FT immunohistochemical analysis in patient tumor tissue)"
FT /evidence="ECO:0000269|PubMed:31322271"
FT /id="VAR_087522"
FT VARIANT 181..580
FT /note="Missing (in UVM1)"
FT /evidence="ECO:0000269|PubMed:32239153"
FT /id="VAR_087523"
FT VARIANT 255..580
FT /note="Missing (in TPDS2)"
FT /evidence="ECO:0000269|PubMed:30049810"
FT /id="VAR_087524"
FT VARIANT 273
FT /note="A -> S (in dbSNP:rs10342)"
FT /evidence="ECO:0000269|Ref.8"
FT /id="VAR_019357"
FT VARIANT 273
FT /note="A -> T (in dbSNP:rs10342)"
FT /id="VAR_019514"
FT VARIANT 342
FT /note="S -> P (in dbSNP:rs2307289)"
FT /evidence="ECO:0000269|Ref.8"
FT /id="VAR_019358"
FT VARIANT 346
FT /note="E -> K (in dbSNP:rs140693)"
FT /evidence="ECO:0000269|Ref.8"
FT /id="VAR_019359"
FT VARIANT 358
FT /note="I -> T (in dbSNP:rs2307298)"
FT /id="VAR_019515"
FT VARIANT 431..580
FT /note="Missing (in TPDS2)"
FT /evidence="ECO:0000269|PubMed:30049810"
FT /id="VAR_087525"
FT VARIANT 468
FT /note="R -> W (in UVM1; loss of DNA N-glycosylase activity;
FT dbSNP:rs1380952147)"
FT /evidence="ECO:0000269|PubMed:32239153"
FT /id="VAR_087526"
FT VARIANT 546..580
FT /note="Missing (in TPDS2)"
FT /evidence="ECO:0000269|PubMed:30049810"
FT /id="VAR_087527"
FT VARIANT 563..580
FT /note="Missing (in TPDS2 and UVM1)"
FT /evidence="ECO:0000269|PubMed:30049810,
FT ECO:0000269|PubMed:30714079, ECO:0000269|PubMed:35460607"
FT /id="VAR_087528"
FT VARIANT 567
FT /note="Missing (in TPDS2; loss of DNA N-glycosylase
FT activity; dbSNP:rs775848563)"
FT /evidence="ECO:0000269|PubMed:30049810"
FT /id="VAR_087529"
FT VARIANT 568
FT /note="D -> H (in dbSNP:rs2307293)"
FT /evidence="ECO:0000269|Ref.8"
FT /id="VAR_019360"
FT VARIANT 569..580
FT /note="Missing (in UVM1; loss of DNA N-glycosylase
FT activity)"
FT /evidence="ECO:0000269|PubMed:32239153"
FT /id="VAR_087530"
FT MUTAGEN 560
FT /note="D->A: Loss of DNA N-glycosylase activity."
FT /evidence="ECO:0000269|PubMed:30049810"
FT CONFLICT 51
FT /note="E -> G (in Ref. 6; BAG64144)"
FT /evidence="ECO:0000305"
FT CONFLICT 359
FT /note="G -> R (in Ref. 6; BAG64144)"
FT /evidence="ECO:0000305"
FT CONFLICT 387
FT /note="S -> L (in Ref. 6; BAG64144)"
FT /evidence="ECO:0000305"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:4LG7"
FT TURN 101..104
FT /evidence="ECO:0007829|PDB:4LG7"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:4LG7"
FT HELIX 121..130
FT /evidence="ECO:0007829|PDB:4LG7"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:4LG7"
FT HELIX 449..452
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 456..465
FT /evidence="ECO:0007829|PDB:4OFA"
FT TURN 466..468
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 471..484
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 488..491
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 496..503
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 504..506
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 509..525
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 531..533
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 539..548
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 553..555
FT /evidence="ECO:0007829|PDB:4OFA"
FT HELIX 561..577
FT /evidence="ECO:0007829|PDB:4OFA"
SQ SEQUENCE 580 AA; 66051 MW; BF16FB21A34B8E5F CRC64;
MGTTGLESLS LGDRGAAPTV TSSERLVPDP PNDLRKEDVA MELERVGEDE EQMMIKRSSE
CNPLLQEPIA SAQFGATAGT ECRKSVPCGW ERVVKQRLFG KTAGRFDVYF ISPQGLKFRS
KSSLANYLHK NGETSLKPED FDFTVLSKRG IKSRYKDCSM AALTSHLQNQ SNNSNWNLRT
RSKCKKDVFM PPSSSSELQE SRGLSNFTST HLLLKEDEGV DDVNFRKVRK PKGKVTILKG
IPIKKTKKGC RKSCSGFVQS DSKRESVCNK ADAESEPVAQ KSQLDRTVCI SDAGACGETL
SVTSEENSLV KKKERSLSSG SNFCSEQKTS GIINKFCSAK DSEHNEKYED TFLESEEIGT
KVEVVERKEH LHTDILKRGS EMDNNCSPTR KDFTGEKIFQ EDTIPRTQIE RRKTSLYFSS
KYNKEALSPP RRKAFKKWTP PRSPFNLVQE TLFHDPWKLL IATIFLNRTS GKMAIPVLWK
FLEKYPSAEV ARTADWRDVS ELLKPLGLYD LRAKTIVKFS DEYLTKQWKY PIELHGIGKY
GNDSYRIFCV NEWKQVHPED HKLNKYHDWL WENHEKLSLS
//
