7W8D

The structure of Deinococcus radiodurans RuvC

Summary for 7W8D

• Entry DOI: 10.2210/pdb7w8d/pdb
• Descriptor: Crossover junction endodeoxyribonuclease RuvC, MAGNESIUM ION (2 entities in total)
• Functional Keywords: holliday junction resolvase, dnase, dna binding, hydrolase
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 2
• Total formula weight: 39387.99

Authors

Cheng, K. (deposition date: 2021-12-07, release date: 2022-08-17, Last modification date: 2023-11-29)

Primary citation

Sun, Y.,Yang, J.,Xu, G.,Cheng, K.
Biochemical and Structural Study of RuvC and YqgF from Deinococcus radiodurans.
Mbio, 13:e0183422-e0183422, 2022

PubMed Abstract: Deinococcus radiodurans possesses robust DNA damage response and repair abilities, and this is mainly due to its efficient homologous recombination repair system, which incorporates an uncharacterized Holliday junction (HJ) resolution process. D. radiodurans encodes two putative HJ resolvase (HJR) homologs: RuvC (DrRuvC) and YqgF (DrYqgF). Here, both DrRuvC and DrYqgF were identified as essential proteins for the survival of D. radiodurans. The crystal structures and the biochemical properties of DrRuvC and DrYqgF were also studied. DrRuvC crystallized as a homodimer, while DrYqgF crystallized as a monomer. DrRuvC could preferentially cleave HJ at the consensus 5'-(G/C)TC↓(G/C)-3' sequence and could prefer using Mn for catalysis , which would be different from the preferences of the other previously characterized RuvCs. On the other hand, DrYqgF was identified as a Mn-dependent RNA 5'-3' exo/endonuclease with a sequence preference for poly(A) and without any HJR activity. Deinococcus radiodurans is one of the most radioresistant bacteria in the world due to its robust DNA damage response and repair abilities, which are contributed by its efficient homologous recombination repair system. However, the late steps of homologous recombination, especially the Holliday junction (HJ) resolution process, have not yet been well-studied in D. radiodurans. We characterized the structural and biochemical features of the two putative HJ resolvases, DrRuvC and DrYqgF, in D. radiodurans. It was identified that DrRuvC and DrYqgF exhibit HJ resolvase (HJR) activity and RNA exo/endonuclease activity, respectively. Furthermore, both DrRuvC and DrYqgF digest substrates in a sequence-specific manner with a preferred sequence that is different from those of the other characterized RuvCs or YqgFs. Our findings provide new insights into the HJ resolution process and reveal a novel RNase involved in RNA metabolism in D. radiodurans.

PubMed: 36000732
DOI: 10.1128/mbio.01834-22

Experimental method

X-RAY DIFFRACTION (2.75016129042 Å)