https://repository.kopri.re.kr/handle/201206/15872 Mon, 13 Apr 2026 23:03:30 GMT 2026-04-13T23:03:30Z https://repository.kopri.re.kr/handle/201206/16247 Title: Structural insights into the role of NahX from Pseudomonas sp. MC1 in the naphthalene degradation pathway Authors: Son, Jonghyeon; Park, Ae Kyung; Shin, Seung Chul; Kim, Dockyu; Kim, Han-Woo Abstract: Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread organic pollutants known for their carcinogenic and mutagenic properties. There is a growing interest in understanding the degradation and detoxification processes of these substances using biological approaches. The bacterium Pseudomonas sp. MC1 contains a metabolic plasmid (81 kb) that encodes enzymes involved in the conversion of naphthalene (the simplest and most soluble PAH) to salicylate. Therein, nahX is a part of the lower naphthalene degradation operon and encodes a 140-amino acid protein. However, the function of NahX remains unclear. To understand its function more clearly, we first determined the three-dimensional structure of NahX. It has a fold similar to that of HbpS, which acts as a sensory component in response to oxidative stress. Biochemical studies have also shown that NahX and HbpS exhibit heme degradation activity and bind to iron ions. Heme degradation and ironsequestering activity protect bacteria against oxidative stress. Previous studies have shown that oxidative stress occurs during naphthalene degradation. Therefore, we postulate that NahX has a defense mechanism against the oxidative stress that may occur during naphthalene metabolism. Sun, 01 Dec 2024 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/16247 2024-12-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/16267 Title: A structure-based mechanism of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (MpaCobU) from Methylocapsa palsarum Authors: Nam, Yewon; Ahn, Yong-Yoon; Kim, Bo-Mi; Kim, Kitae; Lee, Jun Hyuck; Do, Hackwon Abstract: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) is one of the key enzymes that participate in the biosynthesis of cobalamin, specifically lining the lower ligand 5,6-dimethylbenzimidazole in the α-position of cyclic tetrapyrrolidine. During this process, CobU exhibits two distinct activities: kinase and nucleotidyl transferase, using two nucleoside triphosphates. A structural study of CobU from Salmonella typhimurium showed that guanosine triphosphate binding induces a conformational rearrangement of helix 2. This rearrangement decreases the distance between the phosphate binding loop (P-loop) and helix 2, which is important for the subsequent guanylylation step of the reaction. However, these findings provide only partial insights into the mechanism of CobU at the structural level, and the precise molecular details of this mechanism have not yet been studied. As a first step towards elucidating the molecular mechanisms and sequence of events involved in the phosphorylation and guanylylation steps, we report the high-resolution crystal structures of phosphorylated -MpaCobU (1.8 A), the C91S mutant (1.5 A), the guanosine diphosphate complex (1.9 A), and the adenosylcobinamide-phosphate complex (2.6 A) from Methylocapsa palsarum for the first time. High-resolution structures revealed the crucial elements governing the catalytic steps of MpaCobU, thereby contributing to understanding the catalytic mechanism of CobU at the molecular level. ⓒ 2024 The Authors Sun, 01 Sep 2024 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/16267 2024-09-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/16211 Title: Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases Authors: Hwang, Jisub; Lee, Min Ju; Lee, Sung Gu; Do, Hackwon; Lee, Jun Hyuck Abstract: Epoxide hydrolases (EHs), which catalyze the transformation of epoxides to diols, are present in many eukaryotic and prokaryotic organisms. They have recently drawn considerable attention from organic chemists owing to their application in the semisynthesis of enantiospecific diol compounds. Here, we report the crystal structures of BoEH from Bosea sp. PAMC 26642 and CaEH from Caballeronia sordidicola PAMC 26510 at 1.95 and 2.43 angstrom resolution, respectively. Structural analysis showed that the overall structures of BoEH and CaEH commonly possess typical alpha/13 hydrolase fold with the same ring-opening residues (Tyr-Tyr) and conserved catalytic triad residues (Asp-Asp-His). However, the two enzymes were found to have significantly different sequence compositions in the cap domain region, which is involved in the formation of the substrate-binding site in both enzymes. Enzyme activity assay results showed that BoEH had the strongest activity toward the linear aliphatic substrates, whereas CaEH had a higher preference for aromatic- and cycloaliphatic substrates. Computational docking simulations and tunnel identification revealed important residues with different substrate-binding preferences. Collectively, structure comparison studies, together with ligand docking simulation results, suggested that the differences in substrate-binding site residues were highly correlated with substrate specificity. Thu, 01 Feb 2024 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/16211 2024-02-01T00:00:00Z