4R28

MspJI Restriction Endonuclease in Complex with 27-mer Oligonucleotide

Summary for 4R28

• Entry DOI: 10.2210/pdb4r28/pdb
• Related: 4F0P 4F0Q
• Descriptor: Restriction endonuclease, DNA (25-MER), DNA (26-MER) (3 entities in total)
• Functional Keywords: endonuclease, dna methylation dependent, sra domain, epigenetics tool, cytosine methylation-dependent endonuclease, tetrameric endonuclease, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Mycobacterium sp. JLS; More
• Total number of polymer chains: 6
• Total formula weight: 215774.68

Authors

Horton, J.R.,Cheng, X. (deposition date: 2014-08-10, release date: 2014-10-08, Last modification date: 2023-09-20)

Primary citation

Horton, J.R.,Wang, H.,Mabuchi, M.Y.,Zhang, X.,Roberts, R.J.,Zheng, Y.,Wilson, G.G.,Cheng, X.
Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix.
Nucleic Acids Res., 42:12092-12101, 2014

PubMed Abstract: MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.

PubMed: 25262349
DOI: 10.1093/nar/gku871

Experimental method

X-RAY DIFFRACTION (3.055 Å)