Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase

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

doi:10.1007/s12275-020-0089-1

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Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase: Jisub Hwang ^1,2†, Chang-Sook Jeong ^1,2†, Chang Woo Lee ^1†, Seung Chul Shin ³, Han-Woo Kim ^1,2, Sung Gu Lee ^1,2, Ui Joung Youn ^2,3, Chang Sup Lee ⁴, Tae-Jin Oh ^5,6,7, Hak Jun Kim ⁸, Hyun Park ⁹, Hyun Ho Park ¹⁰, Jun Hyuck Lee ^1,2; Journal of Microbiology 2020;58(7):606-613
DOI: https://doi.org/10.1007/s12275-020-0089-1
Published online: April 22, 2020

¹Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ²Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea, ³Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ⁴College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea, ⁵Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea, ⁶Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea, ⁷Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea, ⁸Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea, ⁹Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea, ¹⁰College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea¹Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ²Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea, ³Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea, ⁴College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea, ⁵Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea, ⁶Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea, ⁷Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea, ⁸Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea, ⁹Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea, ¹⁰College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea

Corresponding author: Hyun Park , Tel: +82-32-760-5555,
Hyun Ho Park , Tel: +82-32-760-5555,
Jun Hyuck Lee , Tel: +82-32-760-5555,

Received: 18 February 2020 • Revised: 30 March 2020 • Accepted: 30 March 2020

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Abstract

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.

Keywords: crystal structure; enoyl-CoA isomerase; enoyl- CoA hydratase; X-ray crystallography

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Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase

J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020

DOI: https://doi.org/10.1007/s12275-020-0089-1

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