4kyw

Restriction endonuclease DPNI in complex with two DNA molecules

spinqualitylabelsall models 4kyw, resolution 2.35Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4kyw is a 5 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, NA, ZN NonStd Res: 6MA Related: 4esj Activity: Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Resources: FirstGlance, OCA, RCSB, PDBsum Function [T2D1_STRPN] Recognizes the double-stranded and methylated sequence G(Me)ATC and cleaves after A-2. Publication Abstract from PubMed 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. Structural basis of the methylation specificity of R.DpnI.,Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M Nucleic Acids Res. 2014 Jun 25. pii: gku546. PMID:24966351 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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