type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding / ATP binding Similarity search - Function
: / Restriction endonuclease, type I, methylase subunit / : / Type I restriction modification DNA specificity domain superfamily / : / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction modification DNA specificity domain / Type I restriction enzyme R protein N terminus (HSDR_N) ...: / Restriction endonuclease, type I, methylase subunit / : / Type I restriction modification DNA specificity domain superfamily / : / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / Type I restriction modification DNA specificity domain / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / Type I restriction modification DNA specificity domain / Restriction endonuclease, type I, HsdR / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Type I restriction enzyme EcoR124I/EcoR124II methylase subunit / Type I restriction enzyme EcoR124I/EcoR124II specificity subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit Similarity search - Component
Biological species
Escherichia coli (E. coli)
Method
single particle reconstruction / cryo EM / Resolution: 6.33 Å
Journal: Nat Microbiol / Year: 2020 Title: Structural insights into assembly, operation and inhibition of a type I restriction-modification system. Authors: Yina Gao / Duanfang Cao / Jingpeng Zhu / Han Feng / Xiu Luo / Songqing Liu / Xiao-Xue Yan / Xinzheng Zhang / Pu Gao / Abstract: Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, ...Type I restriction-modification (R-M) systems are widespread in prokaryotic genomes and provide robust protection against foreign DNA. They are multisubunit enzymes with methyltransferase, endonuclease and translocase activities. Despite extensive studies over the past five decades, little is known about the molecular mechanisms of these sophisticated machines. Here, we report the cryo-electron microscopy structures of the representative EcoR124I R-M system in different assemblies (RMS, RMS and MS) bound to target DNA and the phage and mobile genetic element-encoded anti-restriction proteins Ocr and ArdA. EcoR124I can precisely regulate different enzymatic activities by adopting distinct conformations. The marked conformational transitions of EcoR124I are dependent on the intrinsic flexibility at both the individual-subunit and assembled-complex levels. Moreover, Ocr and ArdA use a DNA-mimicry strategy to inhibit multiple activities, but do not block the conformational transitions of the complexes. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into assembly, operation and inhibition mechanisms of type I R-M systems.
History
Deposition
Apr 2, 2020
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Header (metadata) release
May 27, 2020
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Map release
May 27, 2020
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Update
Sep 16, 2020
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Current status
Sep 16, 2020
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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