SNAP output for PDB entry 9c3t [SNAP web server]

PDB-id

9c3t; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein

Method

X-ray (2.37 Å)

Summary

Crystal structure of DNA n6-adenine methyltransferase m.bcejiv from burkholderia cenocepacia in complex with duplex DNA substrate containing gtaaac as recognition sequence

Reference

Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK (2024): "Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation." Nat Commun, 15, 7839. doi: 10.1038/s41467-024-52130-x.

Abstract

Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase called M.BceJIV with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates N6 of the adenine at the fifth base position. Here, we present crystal structures of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structures show not one, but two DNA substrates bound to the M.BceJIV dimer, with each monomer contributing to the recognition of two recognition sequences. We also show that methylation at the two recognition sequences occurs independently, and that the GTWWAC motifs are enriched in intergenic regions in the genomes of B. cenocepacia strains. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.