8RPX

NhoI restriction endonuclease in complex with quadruply methylated DNA target

Summary for 8RPX

• Entry DOI: 10.2210/pdb8rpx/pdb
• Descriptor: Restriction endonuclease (NhoI), DNA (5'-D(*CP*TP*GP*(5CM)P*AP*GP*(5CM)P*TP*C)-3'), DNA(5'-D(*GP*AP*GP*(5CM)P*TP*GP*(5CM)P*AP*GP)-3'), ... (6 entities in total)
• Functional Keywords: dna endonuclease, dna modification, dna binding protein, homodimer, protein-dna complex, dna methylation, hydrolase
• Biological source: Nitrolancea hollandica; More
• Total number of polymer chains: 11
• Total formula weight: 113900.68

Authors

Rafalski, D.,Krakowska, K.,Gilski, M.,Bochtler, M. (deposition date: 2024-01-17, release date: 2024-07-17, Last modification date: 2024-09-04)

Primary citation

Szafran, K.,Rafalski, D.,Skowronek, K.,Wojciechowski, M.,Kazrani, A.A.,Gilski, M.,Xu, S.Y.,Bochtler, M.
Structural analysis of the BisI family of modification dependent restriction endonucleases.
Nucleic Acids Res., 52:9103-9118, 2024

PubMed Abstract: The BisI family of restriction endonucleases is unique in requiring multiple methylated or hydroxymethylated cytosine residues within a short recognition sequence (GCNGC), and in cleaving directly within this sequence, rather than at a distance. Here, we report that the number of modified cytosines that are required for cleavage can be tuned by the salt concentration. We present crystal structures of two members of the BisI family, NhoI and Eco15I_Ntd (N-terminal domain of Eco15I), in the absence of DNA and in specific complexes with tetra-methylated GCNGC target DNA. The structures show that NhoI and Eco15I_Ntd sense modified cytosine bases in the context of double-stranded DNA (dsDNA) without base flipping. In the co-crystal structures of NhoI and Eco15I_Ntd with DNA, the internal methyl groups (G5mCNGC) interact with the side chains of an (H/R)(V/I/T/M) di-amino acid motif near the C-terminus of the distal enzyme subunit and arginine residue from the proximal subunit. The external methyl groups (GCNG5mC) interact with the proximal enzyme subunit, mostly through main chain contacts. Surface plasmon resonance analysis for Eco15I_Ntd shows that the internal and external methyl binding pockets contribute about equally to sensing of cytosine methyl groups.

PubMed: 39041409
DOI: 10.1093/nar/gkae634

Experimental method

X-RAY DIFFRACTION (1.81 Å)