Macromolecule Content

• Total Structure Weight: 8516.75 
• Atom Count: 597 
• Residue Count: 75 
• Unique protein chains: 1

1D9N

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

• DOI: 10.2210/pdb1D9N/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 1999-10-28 Released: 2000-10-28 
• Deposition Author(s): Ohki, I., Shimotake, N., Fujita, N., Nakao, M., Shirakawa, M.

---

Experimental Data Snapshot

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

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

• PubMed: 10581239 
• DOI: 10.1093/emboj/18.23.6653


• 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). 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
METHYL-CPG-BINDING PROTEIN MBD1	A	75	Homo sapiens	Mutation(s): 0  Gene Names: MBD1 (CXXC3, PCM1)
Find proteins for Q9UIS9 (Homo sapiens) Go to Gene View: MBD1 Go to UniProtKB:  Q9UIS9

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 125 
• Conformers Submitted: 25 
• Selection Criteria: structures with the lowest energy 
• Olderado: 1D9N Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-28 
• Released Date: 2000-10-28 
• Deposition Author(s): Ohki, I., Shimotake, N., Fujita, N., Nakao, M., Shirakawa, M.

Revision History 

• Version 1.0: 2000-10-28
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance