|Entry||Database: EMDB / ID: EMD-30186|
|Title||EcoR124I-DNA in the Translocation State|
|Function / homology|
Function and homology information
type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / N-methyltransferase activity / DNA restriction-modification system / DNA binding / ATP binding
Similarity search - Function
Antirestriction protein ArdA, domain 2 / Antirestriction / Antirestriction protein (ArdA) / Antirestriction protein ArdA, domain 3 / Antirestriction protein ArdA, domain 1 / Restriction endonuclease, type I, HsdM / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction modification DNA specificity domain / SWI2/SNF2 ATPase / Restriction endonuclease, type I, HsdR, N-terminal ...Antirestriction protein ArdA, domain 2 / Antirestriction / Antirestriction protein (ArdA) / Antirestriction protein ArdA, domain 3 / Antirestriction protein ArdA, domain 1 / Restriction endonuclease, type I, HsdM / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction modification DNA specificity domain / SWI2/SNF2 ATPase / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / HsdM N-terminal domain / SWI2/SNF2 ATPase / Type-1 restriction enzyme R protein, C-terminal / N6 adenine-specific DNA methyltransferase, N-terminal domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Antirestriction protein ArdA / Type I restriction enzyme EcoR124II M protein / Type-1 restriction enzyme EcoR124II specificity protein / Type I restriction enzyme EcoR124II R protein / Type I restriction enzyme R Protein
Similarity search - Component
|Biological species||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / Resolution: 6.72 Å|
|Authors||Gao P / Gao Y|
|Citation||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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_30186.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.35 Å|
|Symmetry||Space group: 1|
CCP4 map header:
|Entire||Name: EcoR124I-DNA / Number of Components: 1|
-Component #1: protein, EcoR124I-DNA
|Protein||Name: EcoR124I-DNA / Recombinant expression: No|
|Source||Species: Escherichia coli (E. coli)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen Name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 60 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Imaging Mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of Projections: 15236|
|3D reconstruction||Resolution: 6.72 Å / Resolution Method: FSC 0.143 CUT-OFF|
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