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0MBD4_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NameMBD4
DescriptionMethyl-cpg-binding domain protein 4 (ec 3.2.2.-) (methyl-cpg binding protein mbd4) (methyl-cpg binding endonuclease 1) (mismatch-specific dna n-glycosylase).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0005634 nucleus (TAS)
0004520 endodeoxyribonuclease activity (TAS)
0005515 protein binding (IPI)
0003696 satellite DNA binding (TAS)
0006281 DNA repair (TAS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
Methylation at CpG dinucleotide.he most common DNA modification ineukaryotes.as been correlated with gene silencing associated with variousphenomena such as genomic imprinting.ransposon and chromosome Xinactivation.ifferenciation.nd cancer. Effects of DNA methylation aremediated through proteins which bind to symmetrically methylated CpGs. Suchproteins contain a specific domain of ~70 residues.he methyl-CpG-bindingdomain (MBD).hich is linked to additional domains associated with chromatin.uch as the bromodomain.he AT hook motif.he SET domain.r the PHD finger. MBD-containingproteins appear to act as structural proteins.hich recruit a variety ofhistone deacetylase (HDAC) complexes and chromatin remodeling factors.eadingto chromatin compaction and.onsequently.o transcriptional repression. TheMBD of MeCP2.BD1.BD2.BD4 and BAZ2 mediates binding to DNA.n case ofMeCP2.BD1 and MBD2 preferentially to methylated CpG. In case of human MBD3and SETDB1 the MBD has been shown to mediate protein-protein interactions.The MBD folds into an alpha/beta sandwich structure comprising a layer oftwisted beta sheet.acked by another layer formed by the alpha1 helix and ahairpin loop at the C terminus. These layers are bothamphipathic.ith the alpha1 helix and the beta sheet lying parallel and thehydrophobic faces tighly packed against each other. The beta sheet is composedof two long inner strands (beta2 and beta3) sandwiched by two shorter outerstrands (beta1 and beta4) .
  IPR001739:Methyl-CpG binding
Endonuclease III () is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism . The structurally related DNA glycosylase MutYrecognises and excises the mutational intermediate 8-oxoguanine-adenine mispair . The 3-D structures of E. coli endonuclease III and catalytic domain of MutY have been determined. Thestructures contain two all-alpha domains: a sequence-continuous.ix-helix domain (residues 22-132) and a Greek-key.our-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the[Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation patternCys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif isreferred to as a [Fe4S4] cluster loop (FCL) . Two DNA-binding motifs have been proposed.ne at either end of theinterdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see). The primary role of the iron-sulphur cluster appears toinvolve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop ofthe FCL motif . The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III.nd DNA glycosylase MutY.n A/G-specific adenine glycosylase. Both of these enzymes have a C terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II .-oxoguanine DNA glycosylases and other members of the AlkA family.
  IPR003265:HhH-GPD
DNA glycosylases act to repair oxidative damage in DNA. These proteins are redundant as there are several different types of DNA glycosylases that are ale to compensate for one another. Examples include the endonuclease III subfamily.he mismatch glycosylases subfamily.he 3-methyladenine DNA glycosylases I subfamily.nd the DNA repair glycosylases subfamily .The SSF signature in this entry is currently under review. Please be aware that some of the protein hits may be false positives.
  IPR011257:DNA glycosylase
IPR001739:MBD 
Evalue:-34.2365720064371 
Location:79-155IPR003265:HhH-GPD 
Evalue:-4.01322841644287 
Location:461-524
SequencesProtein: MBD4_HUMAN (580 aa)
mRNA: NM_003925
Local Annotation
Synapse Ontology
the generation of action potential at soma of neurons.
sdb:0313 generation of AP at soma  (Evidence:keywords)
KO assignmentK01249
  Level 3 annotation:
    DNA glycosylase
  Level 2 annotation:
    Other replication
     recombination and repair proteins
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 210 residues, 130632482-130633111Exon2: 36 residues, 130634035-130634139Exon3: 52 residues, 130634630-130634780Exon4: 47 residues, 130635382-130635517Exon5: 27 residues, 130635594-130635669Exon6: 290 residues, 130637975-130638841Exon7: 79 residues, 130639252-130639483Exon8: 95 residues, 130641262-130641542Exon9: 2 residues, -Jump to MBD4_HUMAN  
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Loci Cluster (Details)Loci: 3375 130081143-130114646 ~-34K 26440(ACAD9)(+)Loci: 4632 130289107-130323309 ~-34K 26447(-)Loci: 4633 130602854-130630184 ~-27K 26461(-)Loci: 4634 130632482-130641542 ~-9K 26462(MBD4)(-)Loci: 4635 130756707-130808351 ~-52K 26476(PLXND1)(-)Loci: 4636 130849326-131081999 ~-233K 26481(TMCC1)(-)Loci: 3376 131176252-131179470 ~-3K 26482(TRH)(+)Loci: 3374 129927668-130016331 ~-89K 26437(RAB7)(+)Link out to UCSC