4KYW

Restriction endonuclease DPNI in complex with two DNA molecules

Summary for 4KYW

• Entry DOI: 10.2210/pdb4kyw/pdb
• Related: 4ESJ
• Descriptor: Type-2 restriction enzyme DpnI, 5'-(*DC*DTP*DGP*DGP*6MAP*DTP*DCP*DCP*DAP*DG)-3', ZINC ION, ... (6 entities in total)
• Functional Keywords: restriction endonuclease-dna complex, type iim, type iie, restriction enzyme, dpni, methylation dependent, n6-methyladenine, pd-(d/e)xk type endonuclease, winged helix domain, restriction endonuclease, dna binding, hydrolase-dna complex, hydrolase/dna
• Biological source: Streptococcus pneumoniae; More
• Total number of polymer chains: 5
• Total formula weight: 42442.96

Authors

Mierzejewska, K.,Siwek, W.,Czapinska, H.,Skowronek, K.,Bujnicki, J.M.,Bochtler, M. (deposition date: 2013-05-29, release date: 2014-06-04, Last modification date: 2023-09-20)

Primary citation

Mierzejewska, K.,Siwek, W.,Czapinska, H.,Kaus-Drobek, M.,Radlinska, M.,Skowronek, K.,Bujnicki, J.M.,Dadlez, M.,Bochtler, M.
Structural basis of the methylation specificity of R.DpnI.
Nucleic Acids Res., 42:8745-8754, 2014

PubMed Abstract: R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.

PubMed: 24966351
DOI: 10.1093/nar/gku546

Experimental method

X-RAY DIFFRACTION (2.35 Å)