Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop

Chang Woo Lee; Saeyoung Lee; Chang-Sook Jeong; Jisub Hwang; Jeong Ho Chang; In-Geol Choi; T. Doohun Kim; HaJeung Park; Hye-Yeon Kim; Jun Hyuck Lee

doi:10.1007/s12275-020-0292-0

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Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop: Chang Woo Lee ¹, Saeyoung Lee ^2,3, Chang-Sook Jeong ^1,4, Jisub Hwang ^1,4, Jeong Ho Chang ⁵, In-Geol Choi ³, T. Doohun Kim ⁶, HaJeung Park ⁷, Hye-Yeon Kim ^2,8, Jun Hyuck Lee ^1,4; Journal of Microbiology 2020;58(9):772-779.
DOI: https://doi.org/10.1007/s12275-020-0292-0
Published online: September 1, 2020

¹Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ²Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk 34133, Republic of Korea, ³Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea, ⁴Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea, ⁵Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea, ⁶Department of Chemistry, College of Natural Science, Sookmyung Woman’s University, Seoul 04310, Republic of Korea, ⁷X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL 33458, USA, ⁸Center for Convergent Research of Emerging Virus Infection (CEVI), Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea¹Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ²Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk 34133, Republic of Korea, ³Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea, ⁴Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea, ⁵Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea, ⁶Department of Chemistry, College of Natural Science, Sookmyung Woman’s University, Seoul 04310, Republic of Korea, ⁷X-Ray Core, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, FL 33458, USA, ⁸Center for Convergent Research of Emerging Virus Infection (CEVI), Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea

Corresponding author: HaJeung Park , Tel: +82-32-760-5555;,
Hye-Yeon Kim , Tel: +82-32-760-5555;,
Jun Hyuck Lee , Tel: +82-32-760-5555;,

Received: 4 June 2020 • Revised: 30 June 2020 • Accepted: 15 July 2020

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Abstract

In spore forming microbes, germination protease (GPR) plays a key role in the initiation of the germination process. A critical step during germination is the degradation of small acidsoluble proteins (SASPs), which protect spore DNA from external stresses (UV, heat, low temperature, etc.). Inactive zymogen GPR can be activated by autoprocessing of the N-terminal pro-sequence domain. Activated GPR initiates the degradation of SASPs; however, the detailed mechanisms underlying the activation, catalysis, regulation, and substrate recognition of GPR remain elusive. In this study, we determined the crystal structure of GPR from Paenisporosarcina sp. TG-20 (PaGPR) in its inactive form at a resolution of 2.5 Å. Structural analysis showed that the active site of PaGPR is sterically occluded by an inhibitory loop region (residues 202–216). The N-terminal region interacts directly with the self-inhibitory loop region, suggesting that the removal of the N-terminal pro-sequence induces conformational changes, which lead to the release of the self-inhibitory loop region from the active site. In addition, comparative sequence and structural analyses revealed that PaGPR contains two highly conserved Asp residues (D123 and D182) in the active site, similar to the putative aspartic acid protease GPR from Bacillus megaterium. The catalytic domain structure of PaGPR also shares similarities with the sequentially non-homologous proteins HycI and HybD. HycI and HybD are metalloproteases that also contain two Asp (or Glu) residues in their active site, playing a role in metal binding. In summary, our
results
provide useful insights into the activation process of PaGPR and its active conformation.

Keywords: HBV;HIV;circRNAs;ncRNAs;virus

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Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop

J. Microbiol. 2020;58(9):772-779. Published online September 1, 2020

DOI: https://doi.org/10.1007/s12275-020-0292-0

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