1D9N

SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 125 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1.

Ohki, I.Shimotake, N.Fujita, N.Nakao, M.Shirakawa, M.

(1999) EMBO J 18: 6653-6661

  • DOI: 10.1093/emboj/18.23.6653
  • Primary Citation of Related Structures:  
    1D9N

  • PubMed Abstract: 
  • CpG methylation in vertebrates is important for gene silencing, alterations in chromatin structure and genomic stability, and differences in the DNA-methylation status are correlated with imprinting phenomena, carcinogenesis and embryonic development. Methylation signals are interpreted by protein factors that contain shared methyl-CpG-binding domains (MBDs) ...

    CpG methylation in vertebrates is important for gene silencing, alterations in chromatin structure and genomic stability, and differences in the DNA-methylation status are correlated with imprinting phenomena, carcinogenesis and embryonic development. Methylation signals are interpreted by protein factors that contain shared methyl-CpG-binding domains (MBDs). We have determined the solution structure of the MBD of the human methylation-dependent transcriptional repressor MBD1 by multi-dimensional heteronuclear NMR spectroscopy. It folds into an alpha/beta-sandwich structure with characteristic loops. Basic residues conserved in the MBD family are largely confined to one face of this fold and a flexible loop, which together form a large positively charged surface. Site-directed mutagenesis and chemical shift changes upon complexing with a methylated DNA facilitated identification of this surface as the DNA interaction site. In addition to three basic residues, conserved Tyr34 and Asp32 were shown to be important for the DNA binding.


    Related Citations: 
    • A Component of the Transcriptional Repressor MeCP1 Shares a Motif with DNA Methyltransferase and HRX Proteins
      Cross, S.H., Meehan, R.R., Nan, X., Bird, A.
      (1997) Nat Genet 16: 256
    • Methylation-mediated Transcriptional Silencing in Euchromatin by Methyl-CpG Binding Protein MBD1 Isoforms
      Fujita, N., Takebayashi, S., Okumura, K., Kudo, S., Chiba, T., Saya, H., Nakao, M.
      (1999) Mol Cell Biol 19: 6415

    Organizational Affiliation

    Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-CPG-BINDING PROTEIN MBD1A75Homo sapiensMutation(s): 0 
Gene Names: MBD1CXXC3PCM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIS9 (Homo sapiens)
Explore Q9UIS9 
Go to UniProtKB:  Q9UIS9
PHAROS:  Q9UIS9
Entity Groups  
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UniProt GroupQ9UIS9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 125 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Data collection, Database references, Derived calculations