1OPQ

NMR structure of unmethylated GATC site

Summary for 1OPQ

• Entry DOI: 10.2210/pdb1opq/pdb
• Related: 1OQ2 1UAB
• Descriptor: 5'-D(*GP*CP*GP*AP*GP*AP*TP*CP*TP*GP*CP*G)-3', 5'-D(*CP*GP*CP*AP*GP*AP*TP*CP*TP*CP*GP*C)-3' (2 entities in total)
• Functional Keywords: gatc, agatct, oric, dam (dna adenine methyltransferase), seqa, muth, hemimethylation, dna
• Total number of polymer chains: 2
• Total formula weight: 7326.78

Authors

Bae, S.-H.,Cheong, H.-K.,Kang, S.,Hwang, D.S.,Cheong, C.,Choi, B.-S. (deposition date: 2003-03-06, release date: 2004-04-27, Last modification date: 2024-05-29)

Primary citation

Bae, S.-H.,Cheong, H.-K.,Cheong, C.,Kang, S.,Hwang, D.S.,Choi, B.-S.
Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition
J.Biol.Chem., 278:45987-45993, 2003

PubMed Abstract: 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.

PubMed: 12944412
DOI: 10.1074/jbc.M306038200

Experimental method

SOLUTION NMR