UniProtKB - O95243 (MBD4_HUMAN)
Protein
Methyl-CpG-binding domain protein 4
Gene
MBD4
Organism
Homo sapiens (Human)
Status
Functioni
Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.2 Publications
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 560 | By similarity | 1 |
GO - Molecular functioni
- DNA binding Source: GO_Central
- DNA N-glycosylase activity Source: Reactome
- endodeoxyribonuclease activity Source: ProtInc
- pyrimidine-specific mismatch base pair DNA N-glycosylase activity Source: MGI
- satellite DNA binding Source: ProtInc
GO - Biological processi
- depyrimidination Source: Reactome
- DNA repair Source: ProtInc
- response to estradiol Source: Ensembl
Keywordsi
Molecular function | DNA-binding, Hydrolase |
Biological process | DNA damage, DNA repair |
Enzyme and pathway databases
PathwayCommonsi | O95243 |
Reactomei | R-HSA-110328, Recognition and association of DNA glycosylase with site containing an affected pyrimidine R-HSA-110329, Cleavage of the damaged pyrimidine R-HSA-110357, Displacement of DNA glycosylase by APEX1 |
Names & Taxonomyi
Protein namesi | Recommended name: Methyl-CpG-binding domain protein 4 (EC:3.2.2.-)Alternative name(s): Methyl-CpG-binding endonuclease 1 Methyl-CpG-binding protein MBD4 Mismatch-specific DNA N-glycosylase |
Gene namesi | Name:MBD4 Synonyms:MED1 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:6919, MBD4 |
MIMi | 603574, gene |
neXtProti | NX_O95243 |
VEuPathDBi | HostDB:ENSG00000129071.9 |
Subcellular locationi
Nucleus
Nucleus
- nuclear speck Source: HPA
- nucleoplasm Source: Reactome
- nucleus Source: GO_Central
Keywords - Cellular componenti
NucleusPathology & Biotechi
Organism-specific databases
DisGeNETi | 8930 |
OpenTargetsi | ENSG00000129071 |
PharmGKBi | PA30663 |
Miscellaneous databases
Pharosi | O95243, Tbio |
Genetic variation databases
BioMutai | MBD4 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000096264 | 1 – 580 | Methyl-CpG-binding domain protein 4Add BLAST | 580 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 318 | PhosphoserineCombined sources | 1 | |
Modified residuei | 428 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
EPDi | O95243 |
jPOSTi | O95243 |
MassIVEi | O95243 |
MaxQBi | O95243 |
PaxDbi | O95243 |
PeptideAtlasi | O95243 |
PRIDEi | O95243 |
ProteomicsDBi | 19871 50740 [O95243-1] 50741 [O95243-2] 50742 [O95243-3] 61389 |
TopDownProteomicsi | O95243-3 [O95243-3] |
PTM databases
iPTMneti | O95243 |
MetOSitei | O95243 |
PhosphoSitePlusi | O95243 |
Expressioni
Gene expression databases
Bgeei | ENSG00000129071, Expressed in secondary oocyte and 260 other tissues |
ExpressionAtlasi | O95243, baseline and differential |
Genevisiblei | O95243, HS |
Organism-specific databases
HPAi | ENSG00000129071, Low tissue specificity |
Interactioni
Subunit structurei
Interacts with MLH1.
2 PublicationsBinary interactionsi
Hide detailsO95243
With | #Exp. | IntAct |
---|---|---|
FADD [Q13158] | 6 | EBI-348011,EBI-494804 |
Isoform 2 [O95243-2]
With | #Exp. | IntAct |
---|---|---|
GRN [P28799] | 3 | EBI-6448717,EBI-747754 |
HTT [P42858] | 19 | EBI-6448717,EBI-466029 |
MLH1 [P40692] | 3 | EBI-6448717,EBI-744248 |
NAT2 [P11245] | 3 | EBI-6448717,EBI-9057228 |
WFS1 [O76024] | 3 | EBI-6448717,EBI-720609 |
Protein-protein interaction databases
BioGRIDi | 114444, 31 interactors |
IntActi | O95243, 24 interactors |
MINTi | O95243 |
STRINGi | 9606.ENSP00000249910 |
Miscellaneous databases
RNActi | O95243, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
BMRBi | O95243 |
SMRi | O95243 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | O95243 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 76 – 148 | MBDPROSITE-ProRule annotationAdd BLAST | 73 |
Phylogenomic databases
eggNOGi | KOG4161, Eukaryota |
GeneTreei | ENSGT00530000063687 |
HOGENOMi | CLU_034167_0_0_1 |
InParanoidi | O95243 |
OMAi | TRSRWKK |
OrthoDBi | 1574293at2759 |
PhylomeDBi | O95243 |
TreeFami | TF329176 |
Family and domain databases
InterProi | View protein in InterPro IPR016177, DNA-bd_dom_sf IPR011257, DNA_glycosylase IPR017352, MBD4 IPR001739, Methyl_CpG_DNA-bd |
Pfami | View protein in Pfam PF01429, MBD, 1 hit |
PIRSFi | PIRSF038005, Methyl_CpG_bd_MBD4, 1 hit |
SMARTi | View protein in SMART SM00391, MBD, 1 hit |
SUPFAMi | SSF48150, SSF48150, 1 hit SSF54171, SSF54171, 1 hit |
PROSITEi | View protein in PROSITE PS50982, MBD, 1 hit |
s (5+)i Sequence
Sequence statusi: Complete.
This entry describes 5 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 5 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All
Isoform 1 (identifier: O95243-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MGTTGLESLS LGDRGAAPTV TSSERLVPDP PNDLRKEDVA MELERVGEDE
60 70 80 90 100
EQMMIKRSSE CNPLLQEPIA SAQFGATAGT ECRKSVPCGW ERVVKQRLFG
110 120 130 140 150
KTAGRFDVYF ISPQGLKFRS KSSLANYLHK NGETSLKPED FDFTVLSKRG
160 170 180 190 200
IKSRYKDCSM AALTSHLQNQ SNNSNWNLRT RSKCKKDVFM PPSSSSELQE
210 220 230 240 250
SRGLSNFTST HLLLKEDEGV DDVNFRKVRK PKGKVTILKG IPIKKTKKGC
260 270 280 290 300
RKSCSGFVQS DSKRESVCNK ADAESEPVAQ KSQLDRTVCI SDAGACGETL
310 320 330 340 350
SVTSEENSLV KKKERSLSSG SNFCSEQKTS GIINKFCSAK DSEHNEKYED
360 370 380 390 400
TFLESEEIGT KVEVVERKEH LHTDILKRGS EMDNNCSPTR KDFTGEKIFQ
410 420 430 440 450
EDTIPRTQIE RRKTSLYFSS KYNKEALSPP RRKAFKKWTP PRSPFNLVQE
460 470 480 490 500
TLFHDPWKLL IATIFLNRTS GKMAIPVLWK FLEKYPSAEV ARTADWRDVS
510 520 530 540 550
ELLKPLGLYD LRAKTIVKFS DEYLTKQWKY PIELHGIGKY GNDSYRIFCV
560 570 580
NEWKQVHPED HKLNKYHDWL WENHEKLSLS
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketD6RBI7 | D6RBI7_HUMAN | Methyl-CpG-binding domain protein 4 | MBD4 | 52 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 51 | E → G in BAG64144 (PubMed:14702039).Curated | 1 | |
Sequence conflicti | 359 | G → R in BAG64144 (PubMed:14702039).Curated | 1 | |
Sequence conflicti | 387 | S → L in BAG64144 (PubMed:14702039).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_029306 | 61 | C → R. Corresponds to variant dbSNP:rs2307296Ensembl. | 1 | |
Natural variantiVAR_019357 | 273 | A → S1 PublicationCorresponds to variant dbSNP:rs10342Ensembl. | 1 | |
Natural variantiVAR_019514 | 273 | A → T. Corresponds to variant dbSNP:rs10342Ensembl. | 1 | |
Natural variantiVAR_019358 | 342 | S → P1 PublicationCorresponds to variant dbSNP:rs2307289Ensembl. | 1 | |
Natural variantiVAR_019359 | 346 | E → K1 PublicationCorresponds to variant dbSNP:rs140693Ensembl. | 1 | |
Natural variantiVAR_019515 | 358 | I → T. Corresponds to variant dbSNP:rs2307298Ensembl. | 1 | |
Natural variantiVAR_019360 | 568 | D → H1 PublicationCorresponds to variant dbSNP:rs2307293Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_054845 | 83 – 401 | RKSVP…KIFQE → Q in isoform 4. 1 PublicationAdd BLAST | 319 | |
Alternative sequenceiVSP_010816 | 395 – 400 | Missing in isoform 2. 2 Publications | 6 | |
Alternative sequenceiVSP_010817 | 539 – 540 | KY → AP in isoform 3. 1 Publication | 2 | |
Alternative sequenceiVSP_010818 | 541 – 580 | Missing in isoform 3. 1 PublicationAdd BLAST | 40 | |
Alternative sequenceiVSP_054846 | 557 – 580 | HPEDH…KLSLS → RLTPIHNSAHLVSEAK in isoform 5. 1 PublicationAdd BLAST | 24 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF072250 mRNA Translation: AAC68879.1 AF120999, AF120997, AF120998 Genomic DNA Translation: AAD50374.1 AF114784 mRNA Translation: AAD22195.1 AM180876 mRNA Translation: CAJ55826.1 AF532602 mRNA Translation: AAP97338.1 AK303013 mRNA Translation: BAG64144.1 CR450305 mRNA Translation: CAG29301.1 AF494057 Genomic DNA Translation: AAM00008.1 AL449212 Genomic DNA No translation available. CH471052 Genomic DNA Translation: EAW79251.1 CH471052 Genomic DNA Translation: EAW79253.1 CH471052 Genomic DNA Translation: EAW79254.1 CH471052 Genomic DNA Translation: EAW79255.1 BC011752 mRNA Translation: AAH11752.1 |
CCDSi | CCDS3058.1 [O95243-1] CCDS63766.1 [O95243-5] CCDS63767.1 [O95243-3] CCDS63768.1 [O95243-2] CCDS63769.1 [O95243-6] |
RefSeqi | NP_001263199.1, NM_001276270.1 [O95243-2] NP_001263200.1, NM_001276271.1 [O95243-5] NP_001263201.1, NM_001276272.1 [O95243-3] NP_001263202.1, NM_001276273.1 [O95243-6] NP_003916.1, NM_003925.2 [O95243-1] |
Genome annotation databases
Ensembli | ENST00000249910; ENSP00000249910; ENSG00000129071 [O95243-1] ENST00000393278; ENSP00000376959; ENSG00000129071 [O95243-6] ENST00000429544; ENSP00000394080; ENSG00000129071 [O95243-2] ENST00000503197; ENSP00000424873; ENSG00000129071 [O95243-3] ENST00000507208; ENSP00000422327; ENSG00000129071 [O95243-5] |
GeneIDi | 8930 |
KEGGi | hsa:8930 |
UCSCi | uc003emh.3, human [O95243-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Web resourcesi
NIEHS-SNPs |
Atlas of Genetics and Cytogenetics in Oncology and Haematology |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF072250 mRNA Translation: AAC68879.1 AF120999, AF120997, AF120998 Genomic DNA Translation: AAD50374.1 AF114784 mRNA Translation: AAD22195.1 AM180876 mRNA Translation: CAJ55826.1 AF532602 mRNA Translation: AAP97338.1 AK303013 mRNA Translation: BAG64144.1 CR450305 mRNA Translation: CAG29301.1 AF494057 Genomic DNA Translation: AAM00008.1 AL449212 Genomic DNA No translation available. CH471052 Genomic DNA Translation: EAW79251.1 CH471052 Genomic DNA Translation: EAW79253.1 CH471052 Genomic DNA Translation: EAW79254.1 CH471052 Genomic DNA Translation: EAW79255.1 BC011752 mRNA Translation: AAH11752.1 |
CCDSi | CCDS3058.1 [O95243-1] CCDS63766.1 [O95243-5] CCDS63767.1 [O95243-3] CCDS63768.1 [O95243-2] CCDS63769.1 [O95243-6] |
RefSeqi | NP_001263199.1, NM_001276270.1 [O95243-2] NP_001263200.1, NM_001276271.1 [O95243-5] NP_001263201.1, NM_001276272.1 [O95243-3] NP_001263202.1, NM_001276273.1 [O95243-6] NP_003916.1, NM_003925.2 [O95243-1] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2MOE | NMR | - | A | 80-148 | [»] | |
3IHO | X-ray | 2.70 | A | 437-574 | [»] | |
4DK9 | X-ray | 2.76 | A | 426-580 | [»] | |
4E9E | X-ray | 1.90 | A | 427-580 | [»] | |
4E9F | X-ray | 1.79 | A | 427-580 | [»] | |
4E9G | X-ray | 2.35 | A | 427-580 | [»] | |
4E9H | X-ray | 3.00 | A | 427-580 | [»] | |
4EA4 | X-ray | 2.00 | A | 427-574 | [»] | |
4EA5 | X-ray | 2.14 | A | 427-580 | [»] | |
4LG7 | X-ray | 2.50 | A | 83-149 | [»] | |
4OFA | X-ray | 1.55 | A | 426-580 | [»] | |
4OFE | X-ray | 2.15 | A | 426-580 | [»] | |
4OFH | X-ray | 2.22 | A | 426-580 | [»] | |
5CHZ | X-ray | 1.83 | A | 426-580 | [»] | |
BMRBi | O95243 | |||||
SMRi | O95243 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 114444, 31 interactors |
IntActi | O95243, 24 interactors |
MINTi | O95243 |
STRINGi | 9606.ENSP00000249910 |
PTM databases
iPTMneti | O95243 |
MetOSitei | O95243 |
PhosphoSitePlusi | O95243 |
Genetic variation databases
BioMutai | MBD4 |
Proteomic databases
EPDi | O95243 |
jPOSTi | O95243 |
MassIVEi | O95243 |
MaxQBi | O95243 |
PaxDbi | O95243 |
PeptideAtlasi | O95243 |
PRIDEi | O95243 |
ProteomicsDBi | 19871 50740 [O95243-1] 50741 [O95243-2] 50742 [O95243-3] 61389 |
TopDownProteomicsi | O95243-3 [O95243-3] |
Protocols and materials databases
ABCDi | O95243, 2 sequenced antibodies |
Antibodypediai | 1087, 216 antibodies |
Genome annotation databases
Ensembli | ENST00000249910; ENSP00000249910; ENSG00000129071 [O95243-1] ENST00000393278; ENSP00000376959; ENSG00000129071 [O95243-6] ENST00000429544; ENSP00000394080; ENSG00000129071 [O95243-2] ENST00000503197; ENSP00000424873; ENSG00000129071 [O95243-3] ENST00000507208; ENSP00000422327; ENSG00000129071 [O95243-5] |
GeneIDi | 8930 |
KEGGi | hsa:8930 |
UCSCi | uc003emh.3, human [O95243-1] |
Organism-specific databases
CTDi | 8930 |
DisGeNETi | 8930 |
GeneCardsi | MBD4 |
HGNCi | HGNC:6919, MBD4 |
HPAi | ENSG00000129071, Low tissue specificity |
MIMi | 603574, gene |
neXtProti | NX_O95243 |
OpenTargetsi | ENSG00000129071 |
PharmGKBi | PA30663 |
VEuPathDBi | HostDB:ENSG00000129071.9 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG4161, Eukaryota |
GeneTreei | ENSGT00530000063687 |
HOGENOMi | CLU_034167_0_0_1 |
InParanoidi | O95243 |
OMAi | TRSRWKK |
OrthoDBi | 1574293at2759 |
PhylomeDBi | O95243 |
TreeFami | TF329176 |
Enzyme and pathway databases
PathwayCommonsi | O95243 |
Reactomei | R-HSA-110328, Recognition and association of DNA glycosylase with site containing an affected pyrimidine R-HSA-110329, Cleavage of the damaged pyrimidine R-HSA-110357, Displacement of DNA glycosylase by APEX1 |
Miscellaneous databases
BioGRID-ORCSi | 8930, 1 hit in 895 CRISPR screens |
ChiTaRSi | MBD4, human |
EvolutionaryTracei | O95243 |
GeneWikii | MBD4 |
GenomeRNAii | 8930 |
Pharosi | O95243, Tbio |
PROi | PR:O95243 |
RNActi | O95243, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000129071, Expressed in secondary oocyte and 260 other tissues |
ExpressionAtlasi | O95243, baseline and differential |
Genevisiblei | O95243, HS |
Family and domain databases
InterProi | View protein in InterPro IPR016177, DNA-bd_dom_sf IPR011257, DNA_glycosylase IPR017352, MBD4 IPR001739, Methyl_CpG_DNA-bd |
Pfami | View protein in Pfam PF01429, MBD, 1 hit |
PIRSFi | PIRSF038005, Methyl_CpG_bd_MBD4, 1 hit |
SMARTi | View protein in SMART SM00391, MBD, 1 hit |
SUPFAMi | SSF48150, SSF48150, 1 hit SSF54171, SSF54171, 1 hit |
PROSITEi | View protein in PROSITE PS50982, MBD, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | MBD4_HUMAN | |
Accessioni | O95243Primary (citable) accession number: O95243 Secondary accession number(s): B4DZN2 Q96F09 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 19, 2004 |
Last sequence update: | May 1, 1999 | |
Last modified: | February 10, 2021 | |
This is version 169 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Human chromosome 3
Human chromosome 3: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references