- 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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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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993
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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
- Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier
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Chang Woo Lee , Sun-Ha Park , Sung Gu Lee , Seung Chul Shin , Se Jong Han , Han-Woo Kim , Hyun Ho Park , Sunghwan Kim , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee
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J. Microbiol. 2017;55(6):464-474. Published online March 9, 2017
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DOI: https://doi.org/10.1007/s12275-017-6599-9
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930
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The two-component phosphorelay system is the most pre-valent mechanism for sensing and transducing environ-mental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the long- term survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key re-sponse regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regu-latory N-terminal phospho-receiver domain and a DNA- binding C-terminal activator domain. We solved the three- dimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearo-thermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the me-chanism of phosphorylation-dependent activation unique to Spo0A.
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Citations
Citations to this article as recorded by - Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile
Michael A. DiCandia, Adrianne N. Edwards, Joshua B. Jones, Grace L. Swaim, Brooke D. Mills, Shonna M. McBride
Journal of Molecular Biology.2022; 434(13): 167641. CrossRef
- Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii
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Hackwon Do , Chang Woo Lee , Sung Gu Lee , Hara Kang , Chul Min Park , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee
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J. Microbiol. 2016;54(2):114-121. Published online February 2, 2016
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DOI: https://doi.org/10.1007/s12275-016-5549-2
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921
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The gene product of dddC (Uniprot code G5CZI2), from
the Gram-negative marine bacterium Oceanimonas doudoroffii,
is a methylmalonate-semialdehyde dehydrogenase
(OdoMMSDH) enzyme. MMSDH is a member of the aldehyde
dehydrogenase superfamily, and it catalyzes the NADdependent
decarboxylation of methylmalonate semialdehyde
to propionyl-CoA. We determined the crystal structure
of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules
in the asymmetric unit, six subunits complexed with
NAD, which was carried along the protein purification steps.
OdoMMSDH exists as a stable homodimer in solution; each
subunit consists of three distinct domains: an NAD-binding
domain, a catalytic domain, and an oligomerization domain.
Computational modeling studies of the OdoMMSDH structure
revealed key residues important for substrate recognition
and tetrahedral intermediate stabilization. Two basic residues
(Arg103 and Arg279) and six hydrophobic residues (Phe150,
Met153, Val154, Trp157, Met281, and Phe449) were found to
be important for tetrahedral intermediate binding. Modeling
data also suggested that the backbone amide of Cys280 and
the side chain amine of Asn149 function as the oxyanion
hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and
catalytic mechanism of OdoMMSDH.
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Citations
Citations to this article as recorded by - Where do the electrons go? How numerous redox processes drive phytochemical diversity
Patrick J. Horn
Phytochemistry Reviews.2021; 20(2): 367. CrossRef - Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer
Li-Kai Liu, John J. Tanner
Journal of Molecular Biology.2019; 431(3): 524. CrossRef - Reconstructing the Electron Density of Intermediates of the Hydrolysis of N-Acetylaspartate by Aspartoacylase
M. G. Khrenova, E. D. Kots, A. M. Kulakova, A. V. Nemukhin
Russian Journal of Physical Chemistry A.2019; 93(10): 1873. CrossRef - NAD+ promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1
David A. Korasick, Tommi A. White, Srinivas Chakravarthy, John J. Tanner
FEBS Letters.2018; 592(19): 3229. CrossRef - Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde
Lourdes Gómez-Gómez, Luis F. Pacios, Araceli Diaz-Perales, María Garrido-Arandia, Javier Argandoña, Ángela Rubio-Moraga, Oussama Ahrazem
International Journal of Molecular Sciences.2018; 19(5): 1409. CrossRef - X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC
Matthew Wilding, Colin Scott, Thomas S. Peat, Janet Newman
Acta Crystallographica Section F Structural Biology Communications.2017; 73(1): 24. CrossRef
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