7LO5

cryoEM structure DrdV-DNA complex

Summary for 7LO5

• Entry DOI: 10.2210/pdb7lo5/pdb
• EMDB information: 23461
• Descriptor: Site-specific DNA-methyltransferase (adenine-specific), DNA (28-MER), DNA (27-MER), ... (5 entities in total)
• Functional Keywords: inhibitor, complex, endonuclease, methyl transferase, typeiil rm system, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Deinococcus wulumuqiensis; More
• Total number of polymer chains: 12
• Total formula weight: 546119.23

Authors

Shen, B.W.,Stoddard, B.L. (deposition date: 2021-02-09, release date: 2021-03-17, Last modification date: 2024-03-06)

Primary citation

Shen, B.W.,Quispe, J.D.,Luyten, Y.,McGough, B.E.,Morgan, R.D.,Stoddard, B.L.
Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.
Structure, 29:521-530.e5, 2021

PubMed Abstract: Restriction enzymes that combine methylation and cleavage into a single assemblage and modify one DNA strand are capable of efficient adaptation toward novel targets. However, they must reliably cleave invasive DNA and methylate newly replicated unmodified host sites. One possible solution is to enforce a competition between slow methylation at a single unmodified host target, versus faster cleavage that requires multiple unmodified target sites in foreign DNA to be brought together in a reaction synapse. To examine this model, we have determined the catalytic behavior of a bifunctional type IIL restriction-modification enzyme and determined its structure, via cryoelectron microscopy, at several different stages of assembly and coordination with bound DNA targets. The structures demonstrate a mechanism in which an initial dimer is formed between two DNA-bound enzyme molecules, positioning the endonuclease domain from each enzyme against the other's DNA and requiring further additional DNA-bound enzyme molecules to enable cleavage.

PubMed: 33826880
DOI: 10.1016/j.str.2021.03.012

Experimental method

ELECTRON MICROSCOPY (2.86 Å)