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Structure paper

TitleStructural insights into assembly, operation and inhibition of a type I restriction-modification system.
Journal, issue, pagesNat Microbiol, Vol. 5, Issue 9, Page 1107-1118, Year 2020
Publish dateJun 1, 2020
AuthorsYina Gao / Duanfang Cao / Jingpeng Zhu / Han Feng / Xiu Luo / Songqing Liu / Xiao-Xue Yan / Xinzheng Zhang / Pu Gao /
PubMed AbstractType 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.
External linksNat Microbiol / PubMed:32483229
MethodsEM (single particle)
Resolution3.97 - 7.38 Å
Structure data

30166

7bst

EMDB-30166, PDB-7bst:
EcoR124I-Ocr in the Intermediate State
Method: EM (single particle) / Resolution: 4.37 Å

30180

7bto

EMDB-30180, PDB-7bto:
EcoR124I-ArdA in the Translocation State
Method: EM (single particle) / Resolution: 3.97 Å

30181

7btp

EMDB-30181, PDB-7btp:
EcoR124I-Ocr in Restriction-Alleviation State
Method: EM (single particle) / Resolution: 4.01 Å

30182

7btq

EMDB-30182, PDB-7btq:
EcoR124I-DNA in the Restriction-Alleviation State
Method: EM (single particle) / Resolution: 4.54 Å

30183

7btr

EMDB-30183, PDB-7btr:
EcoR124I-ArdA in the Restriction-Alleviation State
Method: EM (single particle) / Resolution: 4.54 Å

EMDB-30184:
EcoR124I-Ocr in the Translocation State
Method: EM (single particle) / Resolution: 6.17 Å

EMDB-30185:
EcoR124I-DNA in the Intermediate State
Method: EM (single particle) / Resolution: 7.38 Å

EMDB-30186:
EcoR124I-DNA in the Translocation State
Method: EM (single particle) / Resolution: 6.72 Å

EMDB-30187:
EcoR124I MTase-DNA
Method: EM (single particle) / Resolution: 6.33 Å

EMDB-30188:
EcoR124I MTase-ArdA
Method: EM (single particle) / Resolution: 6.3 Å

Source
  • escherichia coli (E. coli)
  • escherichia phage t7 (virus)
  • enterococcus faecalis engen0302 (bacteria)
KeywordsIMMUNE SYSTEM / Cryoelectron microscopy / Innate immune mechanism / Complex

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