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(-) Description

Title :  MOUSE MBD4 GLYCOSYLASE DOMAIN IN COMPLEX WITH DNA CONTAINING A RIBOSE SUGAR
 
Authors :  H. Hashimoto, X. Zhang, X. Cheng
Date :  26 Apr 12  (Deposition) - 11 Jul 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Stable Intermediate, N-Glycosidic Bond, Helix-Hairpin-Helix, Dna Glycosylase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, X. Zhang, X. Cheng
Excision Of Thymine And 5-Hydroxymethyluracil By The Mbd4 Dna Glycosylase Domain: Structural Basis And Implications For Active Dna Demethylation.
Nucleic Acids Res. V. 40 8276 2012
PubMed-ID: 22740654  |  Reference-DOI: 10.1093/NAR/GKS628

(-) 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: PXC1064
    Expression System Taxid: 562
    Fragment: GLYCOSYLASE DOMAIN, UNP RESIDUES 411-554
    Gene: MBD4
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: METHYL-CPG-BINDING PROTEIN MBD4, MISMATCH-SPECIFIC DNA N- GLYCOSYLASE
 
Molecule 2 - DNA (5'-D(*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3')
    Chains: B
    Engineered: YES
    Other Details: OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*CP*AP*TP*GP*(3DR)P*GP*CP*TP*GP*A)-3')
    Chains: C
    Engineered: YES
    Other Details: OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2NI1Ligand/IonNICKEL (II) ION
3UNK1Mod. Residue

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:506 , LEU A:508 , ILE A:511 , DT C:20BINDING SITE FOR RESIDUE NI A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EW4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EW4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EW4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EW4)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ew4 A 411 KWTPPRSPFNLVQEILFHDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYPSAEVARAADWRDVSELLKPLGLYDLRAKTIIKFSDEYLTKQWRYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLS 552
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550  


Chain B from PDB  Type:DNA  Length:11
                                           
                 4ew4 B   1 TCAGCGCATGG  11
                                    10 


Chain C from PDB  Type:DNA  Length:11
                                           
                 4ew4 C  12 CCATGxGCTGA  22
                                 |  21 
                                17-3DR
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  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 4EW4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EW4)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ew4
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  MBD4_MOUSE | Q9Z2D7
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  3.2.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        MBD4_MOUSE | Q9Z2D7: 1ngn 3vxv 3vxx 3vyb 3vyq 4evv 4ew0

(-) Related Entries Specified in the PDB File

1ngn APO-STRUCTURE OF MOUSE MBD4 GLYCOSYLASE DOMAIN
4evv CATALYTIC MUTANT D534N IN COMPLEX WITH A G:T MISMATCH
4ew0 CATALYTIC MUTANT D534N IN COMPLEX CONTAINING A 5- HYDROXYMETHYLURACIL