PDBsum entry 1d9n

Gene regulation

PDB id: 1d9n

Contents

Protein chain

75 a.a. *

* Residue conservation analysis

PDB id:

1d9n

Name:

Gene regulation

Title:

Solution structure of the methyl-cpg-binding domain of the methylation-dependent transcriptional repressor mbd1/pcm1

Structure:

Methyl-cpg-binding protein mbd1. Chain: a. Fragment: methyl-cpg-binding domain of mbd1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

25 models

Authors:

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

Key ref:

I.Ohki et al. (1999). Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1. EMBO J, 18, 6653-6661. PubMed id: 10581239 DOI: 10.1093/emboj/18.23.6653

Date:

28-Oct-99 Release date: 28-Oct-00

Protein chain

Q9UIS9  (MBD1_HUMAN) -  Methyl-CpG-binding domain protein 1 from Homo sapiens

Seq: 605 a.a.

Struc: 75 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/18.23.6653

EMBO J 18:6653-6661 (1999)

PubMed id: 10581239

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

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

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.

Selected figure(s)

Figure 3.
Figure 3 Surface diagrams of MBD1 MBD. (A) The protein surface (Nicholls et al., 1991) viewed in the same orientation as in Figure 2. The conserved basic and acidic residues are colored in blue and green, respectively. The hydrophobic superficial patches made up of the conserved residues are colored in yellow. The location of Ser45 is also indicated. (B) Distribution of the electrostatic potential on the solvent-accessible surface (Nicholls et al., 1991). Blue corresponds to positive potential and red to negative potential.

Figure 6.
Figure 6 Putative DNA binding site of MBD. Stick representation (Koradi et al., 1996) of the MBD with selected conserved residues in the proposed DNA binding site. Basic residues are colored in blue; aromatic residues, yellow; an acidic residue, green. Main chains of residues strongly affected by addition of methyl-CpG DNA are colored in red ( [av]/ [max] >0.1). The molecule is rotated approximately -90° about the vertical axis relative to that shown in Figures 2. B-form DNA is also shown in the left-hand figure, with methyl groups in the symmetric methyl-CpG highlighted in yellow. With the DNA binding site placed in the major groove of the B-form DNA, loop L1 and the linker between strand 4 and helix 1 are located close to the phosphate backbone. The side chains of Tyr34 and Asp32 can come into contact with the methyl-CpG.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6653-6661) copyright 1999.

Figures were selected by an automated process.