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Structure paper

TitleStructure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 3058, Year 2019
Publish dateJul 11, 2019
AuthorsNeha Nirwan / Yuzuru Itoh / Pratima Singh / Sutirtha Bandyopadhyay / Kutti R Vinothkumar / Alexey Amunts / Kayarat Saikrishnan /
PubMed AbstractThe AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation ...The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 Å structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the γ subunit complexed to αβ of F-ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.
External linksNat Commun / PubMed:31296862 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 4.8 Å
Structure data

0310

6hz4

EMDB-0310, PDB-6hz4:
Structure of McrBC without DNA binding domains (one half of the full complex)
Method: EM (single particle) / Resolution: 3.6 Å

0311

6hz5

EMDB-0311, PDB-6hz5:
Structure of McrBC without DNA binding domains (Class 1)
Method: EM (single particle) / Resolution: 4.2 Å

0312

6hz6

EMDB-0312, PDB-6hz6:
Structure of McrBC without DNA binding domains (Class 2)
Method: EM (single particle) / Resolution: 4.3 Å

0313

6hz7

EMDB-0313, PDB-6hz7:
Structure of McrBC without DNA binding domains (Class 3)
Method: EM (single particle) / Resolution: 4.3 Å

0314

6hz8

EMDB-0314, PDB-6hz8:
Structure of McrBC without DNA binding domains (Class 4)
Method: EM (single particle) / Resolution: 4.3 Å

0315

6hz9

EMDB-0315, PDB-6hz9:
Structure of McrBC without DNA binding domains (Class 5)
Method: EM (single particle) / Resolution: 4.8 Å

Chemicals

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

ChemComp-MG:
Unknown entry

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

Source
  • Escherichia coli K-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsDNA BINDING PROTEIN / AAA+ superfamily / restriction enzyme

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