- 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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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
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Mobina Bayatian, Ahmad Ali Pourbabaee, Mohammad Ali Amoozegar
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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
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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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937
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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
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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
- Identification of Proteolytic Bacteria from the Arctic Chukchi Sea Expedition Cruise and Characterization of Cold-active Proteases
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Ha Ju Park , Yung Mi Lee , Sunghui Kim , Ah Ram Wi , Se Jong Han , Han-Woo Kim , Il-Chan Kim , Joung Han Yim , Dockyu Kim
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J. Microbiol. 2014;52(10):825-833. Published online August 27, 2014
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DOI: https://doi.org/10.1007/s12275-014-4226-6
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1,096
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Following collection of seawater samples during an Arctic
Chukchi Sea expedition cruise of the Korean icebreaker
Araon in 2012, a total of 15,696 bacteria were randomly isolated
from Marine Broth 2216 agar plates. Of these, 2,526
(16%) showed proteolytic activity and were identified as
mainly Alteromonas (31%), Staphylococcus (27%), and Pseudoalteromonas
(14%). Among the proteolytic strains, seven
were selected based on their significant ability to grow and
produce a halo on skim milk plates at low temperatures
(<5°C) owing to cold-active proteases. These strains were
affiliated with the genus Pseudoalteromonas and were divided
into three groups based on phylogenetic analysis of the 16S
rRNA genes. Profiling cell membrane fatty acids confirmed
the 16S rRNA-based differentiation and revealed the accordance
between the two analyses. Seven genes for serine protease
precursors were amplified from the corresponding
strains, and based on sequence similarities, these genes were
divided into three groups that were identical to those identified
by the 16S rRNA phylogenetic analysis. Three protease
genes from the representative strains of each group
were composed of 2,127–2,130 bp, encoding 708–709 amino
acids, and these genes yielded products with calculated molecular
weights of approximately 72.3–72.8 kDa. Amino acid
sequence analysis suggested that the precursors are members
of the subtilase serine endo- and exo-peptidase clan and contain
four domains (signal peptide, N-terminal prosequence,
catalytic domain, and two pre-peptidase C-terminal domains).
Upon expression in E. coli, each recombinant protease exhibited
proteolytic activity on zymogram gels.
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Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef - Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef - Proteases from the marine bacteria in the genus Pseudoalteromonas: diversity, characteristics, ecological roles, and application potentials
Xiu-Lan Chen, Yan Wang, Peng Wang, Yu-Zhong Zhang
Marine Life Science & Technology.2020; 2(4): 309. CrossRef - Characterization of balofloxacin-stressed proteomics and identification of balofloxacin-binding proteins pre-peptidase and integration host factor in Edwardsiella tarda
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Journal of Proteomics.2019; 205: 103413. CrossRef - The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology
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