1oq2

From Proteopedia

Revision as of 11:14, 20 March 2008

NMR structure of hemimethylated GATC site

Overview

DNA methylation occurs in most organisms from bacteria to mammals and provides a mechanism for epigenetic control of a variety of cellular processes. In Escherichia coli, most of the N6 positions in adenines found in the sequence GATC are methylated by DNA adenine methyltransferase. After DNA replication, the GATC sites exist transiently in the hemimethylated state, and the specific recognition of these hemimethylated GATC sites is essential for several processes, including sequestration of the site of replication initiation by the SeqA protein, strand discrimination in DNA mismatch repair by the MutH protein, and transcription of several genes. Here, we characterize the solution structure and dynamics of two dodecamer DNA duplexes that each contains a single GATC site in either unmethylated or hemimethylated state. We found that the N6-methylated adenine of a hemimethylated GATC site undergoes a slow trans-cis interconversion. The release of a tightly bound cation from hemimethylated DNA explains the instability of this structure. In addition, quantitative structural analysis revealed that hemimethylated DNA has unusual backbone structures and a remarkably narrow major groove. These dynamic and structural features provide insights into the specific recognition of hemimethylated GATC sites by the SeqA protein.

About this Structure

1OQ2 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition., Bae SH, Cheong HK, Cheong C, Kang S, Hwang DS, Choi BS, J Biol Chem. 2003 Nov 14;278(46):45987-93. Epub 2003 Aug 27. PMID:12944412

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