6GCD

DNA binding domain of restriction endonuclease McrBC in complex with 5-hydroxymethylcytosine DNA

Summary for 6GCD

• Entry DOI: 10.2210/pdb6gcd/pdb
• Descriptor: 5-methylcytosine-specific restriction enzyme B, DNA (5'-D(*GP*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3'), ... (4 entities in total)
• Functional Keywords: 5-hydroxymethylcytosine, restriction endonuclease, mcrbc, base flipping, dna binding protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 46858.91

Authors

Sasnauskas, G.,Manakova, E. (deposition date: 2018-04-17, release date: 2018-09-19, Last modification date: 2024-01-17)

Primary citation

Zagorskaite, E.,Manakova, E.,Sasnauskas, G.
Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
FEBS Lett., 592:3335-3345, 2018

PubMed Abstract: Cytosine modifications expand the information content of genomic DNA in both eukaryotes and prokaryotes, providing means for epigenetic regulation and self versus nonself discrimination. For example, the methyl-directed restriction endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine (5fC), and 4mC, and characterize the relative affinity of McrB-N to various cytosine variants. We find that McrB-N flips out modified bases into a protein pocket and binds cytosine derivatives in the order of descending affinity: 4mC > 5mC > 5hmC ≫ 5fC. We also show that pocket mutations alter the relative preference of McrB-N to 5mC, 5hmC, and 4mC.

PubMed: 30194838
DOI: 10.1002/1873-3468.13244

Experimental method

X-RAY DIFFRACTION (1.8 Å)