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

  • Microbial Physiology and Biochemistry
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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 acid-soluble 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 A. 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 metal-loproteases 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.

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Acknowledgments

We would like to thank the staff at the X-ray core facility of Korea Basic Science Institute (KBSI) (Ochang, Korea) and that at BL-5C of the Pohang Accelerator Laboratory (Pohang, Korea) for their kind help and support during data collection. This work was supported by the Korea Polar Research Institute (KOPRI; grant numbers PM20030 and PE20040), the Korea Basic Science Institute (grant numbers C030130, PN2019122), and the National Research Council of Science & Technology (CRC-16-01-KRICT).

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Authors and Affiliations

Authors

Contributions

Chang Woo Lee: Investigation, visualization, writing — original draft. Saeyoung Lee: Data curation, writing — original draft. Chang-Sook Jeong: Data curation, investigation. Jisub Hwang: Resources, investigation. Jeong Ho Chang: Methodology, Investigation. In-Geol Choi: Investigation. T. Doohun Kim: Validation, investigation. HaJeung Park: Writing — review & editing. Hye-Yeon Kim: Supervision, writing — review & editing, acquisition of funding. Jun Hyuck Lee: Supervision, project administration, acquisition of funding, writing — review & editing

Corresponding authors

Correspondence to HaJeung Park, Hye-Yeon Kim or Jun Hyuck Lee.

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The authors declare no conflict of interest.

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Lee, C.W., Lee, S., Jeong, CS. et al. Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop. J Microbiol. 58, 772–779 (2020). https://doi.org/10.1007/s12275-020-0292-0

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

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