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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYL CPG BINDING DOMAIN OF MBD4 IN COMPLEX WITH THE 5MCG/TG SEQUENCE
 
Authors :  J. Otani, K. Arita, T. Kato, M. Kinoshita, M. Ariyoshi, M. Shirakawa
Date :  21 Sep 12  (Deposition) - 16 Jan 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Methyl Cpg Binding Domain, Protein-Dna Complex, Versatile Base Recognition, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Otani, K. Arita, T. Kato, M. Kinoshita, H. Kimura, I. Suetake, S. Tajima, M. Ariyoshi, M. Shirakawa
Structural Basis Of The Versatile Dna Recognition Ability O The Methyl-Cpg Binding Domain Of Methyl-Cpg Binding Domain Protein 4
J. Biol. Chem. V. 288 6351 2013
PubMed-ID: 23316048  |  Reference-DOI: 10.1074/JBC.M112.431098

(-) Compounds

Molecule 1 - METHYL-CPG-BINDING DOMAIN PROTEIN 4
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMETHYL CPG BINDING DOMAIN, UNP RESIDUES 69-136
    GeneMBD4
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMETHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N- GLYCOSYLASE
 
Molecule 2 - DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)- 3')
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*GP*TP*CP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3')
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ACT3Ligand/IonACETATE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:120 , DC C:13 , DT C:14BINDING SITE FOR RESIDUE ACT A 201
2AC2SOFTWAREGLN A:101 , ASN A:118 , GLU A:120BINDING SITE FOR RESIDUE ACT A 202
3AC3SOFTWAREGLN A:83 , ARG A:84 , HOH A:318 , DC C:3 , DT C:4BINDING SITE FOR RESIDUE EDO A 203
4AC4SOFTWAREGLY A:76 , GLU A:78 , ILE A:98 , SER A:99 , DA B:14BINDING SITE FOR RESIDUE EDO A 204
5AC5SOFTWARECYS A:75 , GLY A:76 , TRP A:77BINDING SITE FOR RESIDUE EDO A 205
6AC6SOFTWARELYS A:104 , PHE A:105 , ACT B:101BINDING SITE FOR RESIDUE EDO A 206
7AC7SOFTWAREVAL A:132 , LEU A:133 , PRO A:134BINDING SITE FOR RESIDUE EDO A 207
8AC8SOFTWAREEDO A:206 , 5CM B:9 , DG B:10 , HOH B:248BINDING SITE FOR RESIDUE ACT B 101
9AC9SOFTWAREDC B:13 , DT C:2 , DC C:3BINDING SITE FOR RESIDUE EDO C 101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:75 -A:75

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VXV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VXV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VXV)

(-) Exons   (0, 0)

(no "Exon" information available for 3VXV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:65
 aligned with MBD4_MOUSE | Q9Z2D7 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:65
                                    80        90       100       110       120       130     
           MBD4_MOUSE    71 KPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPK 135
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.........eeeeee.....ee.hhhhhhhhhhhhh....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 3vxv A  71 KPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPK 135
                                    80        90       100       110       120       130     

Chain B from PDB  Type:DNA  Length:14
                                              
                 3vxv B   1 GTCACTACcGGACA  14
                                    10    
                                    9-5CM 

Chain C from PDB  Type:DNA  Length:14
                                              
                 3vxv C   1 GTCTGGTAGTGACT  14
                                    10    

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3VXV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VXV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VXV)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MBD4_MOUSE | Q9Z2D7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008263    pyrimidine-specific mismatch base pair DNA N-glycosylase activity    Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apyrimidinic (AP) site.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0007095    mitotic G2 DNA damage checkpoint    A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage.
    GO:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MBD4_MOUSE | Q9Z2D71ngn 3vxx 3vyb 3vyq 4evv 4ew0 4ew4

(-) Related Entries Specified in the PDB File

3vxx 3vyb 3vyq