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TitleHeterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting.
Journal, issue, pagesJ Mol Biol, Vol. 433, Issue 18, Page 167147, Year 2021
Publish dateSep 3, 2021
AuthorsLinxuan Hao / Rui Zhang / Timothy M Lohman /
PubMed AbstractE. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined ...E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17-18 nucleotides and can melt at least 10-11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecB) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecB, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecB. This suggests that the RecB domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecB is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecB is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.
External linksJ Mol Biol / PubMed:34246654 / PubMed Central
MethodsEM (single particle)
Resolution3.6 - 4.5 Å
Structure data

23952

7mr0

EMDB-23952, PDB-7mr0:
Cryo-EM structure of RecBCD with docked RecBNuc and flexible RecD
Method: EM (single particle) / Resolution: 3.7 Å

23953

7mr1

EMDB-23953, PDB-7mr1:
Cryo-EM structure of RecBCD with undocked RecBNuc and flexible RecD C-terminus
Method: EM (single particle) / Resolution: 4.2 Å

23954

7mr2

EMDB-23954, PDB-7mr2:
Cryo-EM structure of RecBCD with undocked RecBNuc and flexible RecD
Method: EM (single particle) / Resolution: 4.3 Å

23955

7mr3

EMDB-23955, PDB-7mr3:
Cryo-EM structure of RecBCD-DNA complex with docked RecBNuc and stabilized RecD
Method: EM (single particle) / Resolution: 3.6 Å

23956

7mr4

EMDB-23956, PDB-7mr4:
Cryo-EM structure of RecBCD-DNA complex with undocked RecBNuc and flexible RecD
Method: EM (single particle) / Resolution: 4.5 Å

Source
  • escherichia coli k12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
  • synthetic construct (others)
KeywordsHYDROLASE / SF1 helicase / complex / DNA repair / motor protein / HYDROLASE/DNA / HYDROLASE-DNA complex

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