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(-) Description

Title :  STRUCTURAL BASIS FOR THYMINE GLYCOSYLASE ACTIVITY ON T:O6-METHYLG MISMATCH BY METHYL-CPG BINDING DOMAIN PROTEIN 4: IMPLICATIONS FOR ROLES OF ARG468 IN MISMATCH RECOGNITION AND CATALYSIS
 
Authors :  H. Ouzon-Shubeita, Y. -L. Lin, S. Lee
Date :  14 Jan 14  (Deposition) - 22 Apr 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Protein-Dna Complex, Mismatch, Thymine Glycosylase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ouzon-Shubeita, Y. -L. Lin, S. Lee
Structure Of Mbd4 Bound To O6Meg:T Mispair Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYL-CPG-BINDING DOMAIN PROTEIN 4
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN OF MBD4
    Gene: MBD4, MED1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METHYL-CPG-BINDING ENDONUCLEASE 1, METHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N-GLYCOSYLASE
 
Molecule 2 - 12-MER DNA(T)
    Chains: C
    Engineered: YES
    Other Details: NATURE SUBSTRATE
    Synthetic: YES
 
Molecule 3 - 12-MER DNA(O6MEG)
    Chains: D
    Engineered: YES
    Other Details: NATURE SUBSTRATE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
16OG1Mod. Nucleotide6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:532 , LEU A:534 , ILE A:537 , DA C:10 , HOH C:102 , HOH C:118BINDING SITE FOR RESIDUE MG A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OFH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OFH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OFH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OFH)

(-) Exons   (0, 0)

(no "Exon" information available for 4OFH)

(-) 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:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ofh A 438 WTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPENHKLNKYHDWLWENHEKLS 578
                                   447       457       467       477       487       497       507       517       527       537       547       557       567       577 


Chain C from PDB  Type:DNA  Length:12
                                            
                 4ofh C   1 CCAGCGTGCAGC  12
                                    10  


Chain D from PDB  Type:DNA  Length:12
                                            
                 4ofh D   1 GCTGCgCGCTGG  12
                                 |  10  
                                 6-6OG
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4OFH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OFH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OFH)

(-) Gene Ontology  (16, 16)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MBD4_HUMAN | O95243: 2moe 3iho 4dk9 4e9e 4e9f 4e9g 4e9h 4ea4 4ea5 4lg7 4ofa 4ofe 5chz

(-) Related Entries Specified in the PDB File

3iho 4e9e 4e9f 4e9g 4ea4 4ea5 4ofa 4ofe