4LD0

T. thermophilus RuvC in complex with Holliday junction substrate

Summary for 4LD0

• Entry DOI: 10.2210/pdb4ld0/pdb
• Descriptor: Crossover junction endodeoxyribonuclease RuvC, DNA 31-MER, DNA 13-MER, ... (4 entities in total)
• Functional Keywords: rnase h fold, nuclease, dna, hydrolase-dna complex, hydrolase/dna
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 5
• Total formula weight: 52965.18

Authors

Gorecka, K.M.,Komorowska, W.,Nowotny, M. (deposition date: 2013-06-24, release date: 2013-09-04, Last modification date: 2024-02-28)

Primary citation

Gorecka, K.M.,Komorowska, W.,Nowotny, M.
Crystal structure of RuvC resolvase in complex with Holliday junction substrate.
Nucleic Acids Res., 41:9945-9955, 2013

PubMed Abstract: 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.

PubMed: 23980027
DOI: 10.1093/nar/gkt769

Experimental method

X-RAY DIFFRACTION (3.75 Å)