- Structural insights into the psychrophilic germinal protease PaGPR and its autoinhibitory loop
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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
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J. Microbiol. 2020;58(9):772-779. Published online September 1, 2020
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DOI: https://doi.org/10.1007/s12275-020-0292-0
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 Abstract
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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.
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Citations
Citations to this article as recorded by  - Crystal structure of human LC8 bound to a peptide from Ebola virus VP35
Dahwan Lim, Ho-Chul Shin, Joon Sig Choi, Seung Jun Kim, Bonsu Ku
Journal of Microbiology.2021; 59(4): 410. CrossRef - Purification and Crystallographic Analysis of a Novel Cold-Active Esterase (HaEst1) from Halocynthiibacter arcticus
Sangeun Jeon, Jisub Hwang, Wanki Yoo, Joo Won Chang, Hackwon Do, Han-Woo Kim, Kyeong Kyu Kim, Jun Hyuck Lee, T. Doohun Kim
Crystals.2021; 11(2): 170. CrossRef
- Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase
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Jisub Hwang , Chang-Sook Jeong , Chang Woo Lee , Seung Chul Shin , Han-Woo Kim , Sung Gu Lee , Ui Joung Youn , Chang Sup Lee , Tae-Jin Oh , Hak Jun Kim , Hyun Park , Hyun Ho Park , Jun Hyuck Lee
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J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020
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DOI: https://doi.org/10.1007/s12275-020-0089-1
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Abstract
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Crystal structures of enoyl-coenzyme A (CoA) isomerase from
Bosea sp. PAMC 26642 (BoECI) and enoyl-CoA hydratase
from Hymenobacter sp. PAMC 26628 (HyECH) were determined
at 2.35 and 2.70 Å resolution, respectively. BoECI
and HyECH are members of the crotonase superfamily and
are enzymes known to be involved in fatty acid degradation.
Structurally, these enzymes are highly similar except for the
orientation of their C-terminal helix domain. Analytical ultracentrifugation
was performed to determine the oligomerization
states of BoECI and HyECH revealing they exist as
trimers in solution. However, their putative ligand-binding
sites and active site residue compositions are dissimilar. Comparative
sequence and structural analysis revealed that the
active site of BoECI had one glutamate residue (Glu135), this
site is occupied by an aspartate in some ECIs, and the active
sites of HyECH had two highly conserved glutamate residues
(Glu118 and Glu138). Moreover, HyECH possesses a salt
bridge interaction between Glu98 and Arg152 near the active
site. This interaction may allow the catalytic Glu118 residue
to have a specific conformation for the ECH enzyme reaction.
This salt bridge interaction is highly conserved in known
bacterial ECH structures and ECI enzymes do not have this
type of interaction. Collectively, our comparative sequential
and structural studies have provided useful information to
distinguish and classify two similar bacterial crotonase superfamily
enzymes.
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Citations
Citations to this article as recorded by - Genome-based characterization of a halotolerant strain, Planococcus antioxidans PAB314, with potential for PAH degradation
Mobina Bayatian, Ahmad Ali Pourbabaee, Mohammad Ali Amoozegar
World Journal of Microbiology and Biotechnology.2026;[Epub] CrossRef - Exploring the Antimicrobial Perspective of Citronella (Cymbopogon nardus) Oil Through GC/MS-based Compound Identification, Molecular Docking, and MD Simulation Insights
Pooja Sankaranarayanan, Aarya Sreedevi, J. Parvathy, Denoj Sebastian, Suchithra Tharamel Vasu
Journal of Computational Biophysics and Chemistry.2026; 25(11): 2711. CrossRef - Breaking aromaticity in the anaerobic degradation pathway of phenanthrene comprises only ATP-independent type III aryl-CoA reductases
Nadia A. Samak, Marvin Häßler, Oliver J. Schmitz, Khadija Adjir, Rainer U. Meckenstock
Communications Biology.2026;[Epub] CrossRef - ECHDC2 inhibits the proliferation of gastric cancer cells by binding with NEDD4 to degrade MCCC2 and reduce aerobic glycolysis
Jiancheng He, Jianfeng Yi, Li Ji, Lingchen Dai, Yu Chen, Wanjiang Xue
Molecular Medicine.2024;[Epub] CrossRef - Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite
Zhenhong Chen, Bo Song, Hongyu Guo, Dapin Xia, Yidong Cai, Yongjun Wang, Weizhong Zhao
Environmental Research.2023; 227: 115777. CrossRef - Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex
Hyeoncheol Francis Son, Jae-Woo Ahn, Jiyeon Hong, Jihye Seok, Kyeong Sik Jin, Kyung-Jin Kim
Archives of Biochemistry and Biophysics.2022; 730: 109391. CrossRef - Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8
Sivaraman Padavattan, Sneha Jos, Hemanga Gogoi, Bagautdin Bagautdinov
Acta Crystallographica Section F Structural Biology Communications.2021; 77(5): 148. CrossRef
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