6UT3

X-ray structure of Thermococcus gammatolerans McrB AAA+ domain hexamer in P21 symmetry

Summary for 6UT3

• Entry DOI: 10.2210/pdb6ut3/pdb
• Descriptor: GTPase subunit of restriction endonuclease, MAGNESIUM ION, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE (3 entities in total)
• Functional Keywords: aaa protein, gtpase, methylation-dependent restriction, dna binding protein
• Biological source: Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)
• Total number of polymer chains: 6
• Total formula weight: 303077.52

Authors

Niu, Y.,Hosford, C.J.,Chappie, J.S. (deposition date: 2019-10-29, release date: 2020-10-21, Last modification date: 2024-03-06)

Primary citation

Niu, Y.,Suzuki, H.,Hosford, C.J.,Walz, T.,Chappie, J.S.
Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes.
Nat Commun, 11:5907-5907, 2020

PubMed Abstract: 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.

PubMed: 33219217
DOI: 10.1038/s41467-020-19735-4

Experimental method

X-RAY DIFFRACTION (2.95 Å)