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Structure paper

TitleStructural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 5907, Year 2020
Publish dateNov 20, 2020
AuthorsYiming Niu / Hiroshi Suzuki / Christopher J Hosford / Thomas Walz / Joshua S Chappie /
PubMed AbstractMcrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis ...McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.
External linksNat Commun / PubMed:33219217 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.44 - 4.26 Å
Structure data

20865

6ut4

EMDB-20865, PDB-6ut4:
Cryo-EM structure of the asymmetric AAA+ domain hexamer from Thermococcus gammatolerans McrB
Method: EM (single particle) / Resolution: 3.1 Å

20866

6ut5

EMDB-20866, PDB-6ut5:
Cryo-EM structure of the Thermococcus gammatolerans McrBC complex
Method: EM (single particle) / Resolution: 2.44 Å

20867

6ut6

EMDB-20867, PDB-6ut6:
Cryo-EM structure of the Escherichia coli McrBC complex
Method: EM (single particle) / Resolution: 3.28 Å

20868

6ut7

EMDB-20868: Full map of the tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC in C2 symmetry
PDB-6ut7: Fitted model for the tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC
Method: EM (single particle) / Resolution: 4.26 Å

EMDB-20869:
Body 1 for multi-body refinement of the McrB-AAA+ and McrC complex from Thermococcus gammatolerans
Method: EM (single particle) / Resolution: 3.95 Å

EMDB-20870:
Body 2 for multi-body refinement of the McrB-AAA+ and McrC complex from Thermococcus gammatolerans
Method: EM (single particle) / Resolution: 4.1 Å

20871

6ut8

EMDB-20871: Combined map of the half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC
PDB-6ut8: Refined half-complex from tetradecameric assembly of Thermococcus gammatolerans McrB AAA+ hexamers with bound McrC
Method: EM (single particle) / Resolution: 3.68 Å

PDB-6ut3:
X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

ChemComp-HOH:
WATER / Water

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

Source
  • thermococcus gammatolerans (archaea)
  • escherichia coli (strain k12) (bacteria)
  • thermococcus gammatolerans (strain dsm 15229 / jcm 11827 / ej3) (archaea)
KeywordsDNA BINDING PROTEIN / AAA protein / GTPase / Methylation-dependent restriction / Endonuclease

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