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Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.

ABSTRACT: The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage ? viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation.

SUBMITTER: Laxmikanthan G

PROVIDER: S-EPMC4880445 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.

Laxmikanthan Gurunathan G Xu Chen C Brilot Axel F AF Warren David D Steele Lindsay L Seah Nicole N Tong Wenjun W Grigorieff Nikolaus N Landy Arthur A Van Duyne Gregory D GD

eLife 20160525

The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the ...[more]

PMID: 27223329

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Crystal structure of RuvC resolvase in complex with Holliday junction substrate.

Project description:The key intermediate in genetic recombination is the Holliday junction (HJ), a four-way DNA structure. At the end of recombination, HJs are cleaved by specific nucleases called resolvases. In Gram-negative bacteria, this cleavage is performed by RuvC, a dimeric endonuclease that belongs to the retroviral integrase superfamily. Here, we report the first crystal structure of RuvC in complex with a synthetic HJ solved at 3.75 Å resolution. The junction in the complex is in an unfolded 2-fold symmetrical conformation, in which the four arms point toward the vertices of a tetrahedron. The two scissile phosphates are located one nucleotide from the strand exchange point, and RuvC approaches them from the minor groove side. The key protein-DNA contacts observed in the structure were verified using a thiol-based site-specific cross-linking approach. Compared with known complex structures of the phage resolvases endonuclease I and endonuclease VII, the RuvC structure exhibits striking differences in the mode of substrate binding and location of the cleavage site.

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Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.

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Synergistic effect of ATP for RuvA-RuvB-Holliday junction DNA complex formation.

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Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination.

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