4XQK

ATP-dependent Type ISP restriction-modification enzyme LlaBIII bound to DNA

Summary for 4XQK

• Entry DOI: 10.2210/pdb4xqk/pdb
• Descriptor: LlaBIII, DNA (28-MER), POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: atp-dependent restriction-modification enzyme, type isp restriction-modification enzyme, atpase, hydrolase-dna complex, hydrolase/dna
• Biological source: Lactococcus lactis subsp. cremoris; More
• Total number of polymer chains: 6
• Total formula weight: 394904.64

Authors

Chand, M.K.,Saikrishnan, K. (deposition date: 2015-01-19, release date: 2015-09-16, Last modification date: 2024-03-20)

Primary citation

Chand, M.K.,Nirwan, N.,Diffin, F.M.,Aelst, K.V.,Kulkarni, M.,Pernstich, C.,Szczelkun, M.D.,Saikrishnan, K.
Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes
Nat.Chem.Biol., 11:870-877, 2015

PubMed Abstract: Production of endonucleolytic double-strand DNA breaks requires separate strand cleavage events. Although catalytic mechanisms for simple, dimeric endonucleases are known, there are many complex nuclease machines that are poorly understood. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide after convergent ATP-driven translocation. We report the 2.7-Å resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are located upstream of the direction of translocation, an observation inconsistent with simple nuclease-domain dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex in which the nuclease domains are distal. Sequencing of the products of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand-nicking events combine to produce DNA scission.

PubMed: 26389736
DOI: 10.1038/nchembio.1926

Experimental method

X-RAY DIFFRACTION (2.7 Å)