3SSC

DNA binding domain of restriction endonuclease bound to DNA

Summary for 3SSC

• Entry DOI: 10.2210/pdb3ssc/pdb
• Related: 3SSD 3SSE
• Descriptor: 5-methylcytosine-specific restriction enzyme B, DNA (5'-D(*TP*GP*AP*GP*AP*(5CM)P*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*AP*GP*CP*TP*AP*(5CM)P*CP*GP*GP*TP*CP*TP*C)-3'), ... (4 entities in total)
• Functional Keywords: protein-dna complex, restriction endonuclease, 5-methylcytosine, base flipping complex, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 47292.08

Authors

Sukackaite, R.,Grazulis, S.,Siksnys, V. (deposition date: 2011-07-08, release date: 2012-05-23, Last modification date: 2024-02-28)

Primary citation

Sukackaite, R.,Grazulis, S.,Tamulaitis, G.,Siksnys, V.
The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.
Nucleic Acids Res., 40:7552-7562, 2012

PubMed Abstract: DNA cytosine methylation is a widespread epigenetic mark. Biological effects of DNA methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in different sequence contexts. Until now two different structural mechanisms have been established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination of the 5mC modification is achieved in prokaryotes. Here we report the crystal structure of the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from Escherichia coli. The McrB-N protein shows a novel DNA-binding fold adapted for 5mC-recognition. In the McrB-N structure in complex with methylated DNA, the 5mC base is flipped out from the DNA duplex and positioned within a binding pocket. Base flipping elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol., 64, 557-569]: flipped out 5-hydroxymethylcytosine is accommodated in the binding pocket but there is no room for the glycosylated base. The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds.

PubMed: 22570415
DOI: 10.1093/nar/gks332

Experimental method

X-RAY DIFFRACTION (2.1 Å)