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BIO DESIGN

pISSN 2288-6982
eISSN 2288-7105

Article

Article

Crystallization

Bio Design 2019; 7(4): 94-97

Published online December 30, 2019

© Korean Society for Structural Biology

Purification and preliminary analysis of the nuclease and capping domain of the DNA repair exonuclease SbcD from the Grampositive bacteria Staphylococcus aureus

Jinwook Lee1, Inseong Jo1,3, Aeran Kwon2 and Nam-Chul Ha1,*

1Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul 08826, Republic of Korea 2Department of Herbal Skin Care, College of Herbal Bio-industry, Deagu Haany University, Gyeongsan, Gyeongbuk 38610, Republic of Korea 3Current address: KoBioLabs, Inc., Seoul 08826, Republic of Korea *Correspondence: hanc210@snu.ac.kr

Abstract

The SbcCD complex is the bacterial Mre11-Rad50 homolog, and cleaves blocked DNA ends and hairpins by an ATPdependent endo- and exonuclease activities to repair DNA. The SbcC component consists of an ATP-binding cassettetype nucleotide-binding domain and a flanking coiled-coil insertion containing a dimerization motif. The SbcD component consists of a nuclease and capping domain, a linker region, and a helix-loop-helix (HLH) domain. The structural studies have been in Gram-negative bacteria. It remains to be elucidated the action mechanism at the molecular level, especially in Gram-positive bacteria. Here, we studied the nuclease and capping domain of SbcD from the Gram-positive bacteria Staphylococcus aureus. The protein was overexpressed and purified, and its crystals suitable for the structural study were obtained. We collected X-ray diffraction dataset at a resolution of 3.5 Å. The crystals belong to space group P212121, with unit cell parameters a = 72.6, b = 88.9, and c = 115.8 Å. The molecular replacement trials were failed to determine the structure, and thus we are now growing the Se-Met substituted crystals to solve the crystal structure. This structure will give molecular insights into the DNA repair process mediated by the SbcCD complex, in the Gram-positive bacteria.