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Cho G, Lee J, Kim J. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Nucleic Acids Res 2023; 51:1971-1983. [PMID: 36762482 PMCID: PMC9976899 DOI: 10.1093/nar/gkad048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
The uridine at the 34th position of tRNA, which is able to base pair with the 3'-end codon on mRNA, is usually modified to influence many aspects of decoding properties during translation. Derivatives of 5-methyluridine (xm5U), which include methylaminomethyl (mnm-) or carboxymethylaminomethyl (cmnm-) groups at C5 of uracil base, are widely conserved at the 34th position of many prokaryotic tRNAs. In Gram-negative bacteria such as Escherichia coli, a bifunctional MnmC is involved in the last two reactions of the biosynthesis of mnm5(s2)U, in which the enzyme first converts cmnm5(s2)U to 5-aminomethyl-(2-thio)uridine (nm5(s2)U) and subsequently installs the methyl group to complete the formation of mnm5(s2)U. Although mnm5s2U has been identified in tRNAs of Gram-positive bacteria and plants as well, their genomes do not contain an mnmC ortholog and the gene(s) responsible for this modification is unknown. We discovered that MnmM, previously known as YtqB, is the methyltransferase that converts nm5s2U to mnm5s2U in Bacillus subtilis through comparative genomics, gene complementation experiments, and in vitro assays. Furthermore, we determined X-ray crystal structures of MnmM complexed with anticodon stem loop of tRNAGln. The structures provide the molecular basis underlying the importance of U33-nm5s2U34-U35 as the key determinant for the specificity of MnmM.
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Affiliation(s)
- Gyuhyeok Cho
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jangmin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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Deng J, Lv X, Li J, Du G, Chen J, Liu L. Recent advances and challenges in microbial production of human milk oligosaccharides. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s43393-020-00004-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Mu X, Xu D. QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism. J Mol Model 2020; 26:71. [PMID: 32146530 DOI: 10.1007/s00894-020-4330-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/23/2020] [Indexed: 11/25/2022]
Abstract
Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of Oδ2-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
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Affiliation(s)
- Xia Mu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China. .,Research Center for Material Genome Engineering, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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Li P, Zhang C, Xu D. Molecular dynamics investigations of cello-oligosaccharide recognition by Cel9G-CBM3c from Clostridium cellulovorans. Phys Chem Chem Phys 2018; 20:5235-5245. [PMID: 29399685 DOI: 10.1039/c7cp07175b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The processive mechanism of cellulases against cellulose represents one of the key mechanisms in the conversion of biomass. A reliable model of substrate binding in a multidomain cellulase is a prerequisite for fully understanding this mechanism. In this study, the specificity of the recognition of the polysaccharide by the multidomain endoglucanase Cel9G from Clostridium cellulovorans was investigated by molecular dynamics simulations. Aromatic ring-containing residues were found to be critical for stabilizing the substrate. The calculated subtotal contributions of polar residues close to the active site, e.g., D58, E244, R315 and D420, also have some critical functions in substrate binding. Unlike other members of the carbohydrate-binding module family, CBM3c alone is shown not to bind cellulose very well, which is also consistent with experimental conclusions.
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Affiliation(s)
- Penghui Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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Xiong J, Zhang C, Xu D. Catalytic mechanism of type C sialidase from Streptococcus pneumoniae: from covalent intermediate to final product. J Mol Model 2018; 24:297. [PMID: 30259133 DOI: 10.1007/s00894-018-3822-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/04/2018] [Indexed: 12/24/2022]
Abstract
Streptococcus pneumoniae is a Gram-positive human pathogenic bacterium, which is the main cause of pneumonia and meningitis in children and the elderly. Three sialidases (or neuraminidases) encoded from Streptococcus pneumoniae could catalyze the cleavage of sialic acid linkages. This mechanism is directly connected with infection, apoptosis, and signaling, and usually considered to be one of the critical virulence factors. Type C neuraminidase (NanC) is unique because its primary product of Neu5Ac2en is considered to be an inhibitor to the other two sialidases. Experimentally, there are two different pathways for the formation mechanism of Neu5Ac2en catalyzed by NanC. In this work, a combined quantum mechanical and molecular mechanical approach was employed in all calculations. Starting from the covalent sialylated intermediate, we first examined the reaction to Neu5Ac2en and found the reaction prefers a direct proton abstraction mechanism rather than the water mediated proton abstraction mechanism. Free energy profiles can confirm that Neu5Ac2en is the major product of NanC. Functional roles of some important residues were also investigated, e.g., D315 acts as the proton acceptor during the formation of Neu5Ac2en, while the general base for the hydrolytic reaction to Neu5Ac. This study can facilitate the understanding of the catalytic mechanism of NanC and has the potential to aid in future inhibitor design studies.
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Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, 610500, People's Republic of China
| | - Chunchun Zhang
- Analytical&Testing Center, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
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Ruthenium-Pincer-Catalyzed Hydrogenation of Lactams to Amino Alcohols. Chem Asian J 2018; 13:2559-2565. [DOI: 10.1002/asia.201800759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/06/2018] [Indexed: 01/07/2023]
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Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, Taguchi H. Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem 2017; 292:7487-7506. [PMID: 28270506 DOI: 10.1074/jbc.m116.762724] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/04/2017] [Indexed: 11/06/2022] Open
Abstract
β-1,2-Glucan is an extracellular cyclic or linear polysaccharide from Gram-negative bacteria, with important roles in infection and symbiosis. Despite β-1,2-glucan's importance in bacterial persistence and pathogenesis, only a few reports exist on enzymes acting on both cyclic and linear β-1,2-glucan. To this end, we purified an endo-β-1,2-glucanase to homogeneity from cell extracts of the environmental species Chitinophaga arvensicola, and an endo-β-1,2-glucanase candidate gene (Cpin_6279) was cloned from the related species Chitinophaga pinensis The Cpin_6279 protein specifically hydrolyzed linear β-1,2-glucan with polymerization degrees of ≥5 and a cyclic counterpart, indicating that Cpin_6279 is an endo-β-1,2-glucananase. Stereochemical analysis demonstrated that the Cpin_6279-catalyzed reaction proceeds via an inverting mechanism. Cpin_6279 exhibited no significant sequence similarity with known glycoside hydrolases (GHs), and thus the enzyme defines a novel GH family, GH144. The crystal structures of the ligand-free and complex forms of Cpin_6279 with glucose (Glc) and sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) determined up to 1.7 Å revealed that it has a large cavity appropriate for polysaccharide degradation and adopts an (α/α)6-fold slightly similar to that of GH family 15 and 8 enzymes. Mutational analysis indicated that some of the highly conserved acidic residues in the active site are important for catalysis, and the Cpin_6279 active-site architecture provided insights into the substrate recognition by the enzyme. The biochemical characterization and crystal structure of this novel GH may enable discovery of other β-1,2-glucanases and represent a critical advance toward elucidating structure-function relationships of GH enzymes.
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Affiliation(s)
- Koichi Abe
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657.,the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Masahiro Nakajima
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510,
| | | | - Hiroki Matsunaga
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Shinji Kamisuki
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510.,the School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuoh-ku, Sagamihara 229-8501
| | - Takanori Nihira
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Yuta Takahashi
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Naohisa Sugimoto
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Akimasa Miyanaga
- the Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroyuki Nakai
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Takatoshi Arakawa
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Shinya Fushinobu
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Hayao Taguchi
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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Xiong J, Xu D. Insights into the Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. J Phys Chem B 2017; 121:931-941. [DOI: 10.1021/acs.jpcb.6b10501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Xiong
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry, College of Chemistry and ‡Geonome Research
Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
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Sugiyama Y, Gotoh A, Katoh T, Honda Y, Yoshida E, Kurihara S, Ashida H, Kumagai H, Yamamoto K, Kitaoka M, Katayama T. Introduction of H-antigens into oligosaccharides and sugar chains of glycoproteins using highly efficient 1,2-α-l-fucosynthase. Glycobiology 2016; 26:1235-1247. [DOI: 10.1093/glycob/cww085] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022] Open
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Li F, Xu D. Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae. J Mol Model 2015; 21:196. [PMID: 26169310 DOI: 10.1007/s00894-015-2724-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 11/25/2022]
Abstract
Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding mode, we in this work further investigate the functional role of active site arginine residue, R462, in the degradation of hyaluronan. The site directed mutagenesis simulation of R462A and R462Q were modeled using a combined quantum mechanical and molecular mechanical method. The overall substrate binding features upon mutations do not have significant changes. The energetic profiles for the reaction processes are essentially the same as that in wild type enzyme, but significant activation barrier height changes can be observed. Both mutants were shown to accelerate the overall enzymatic activity, e.g., R462A can reduce the barrier height by about 2.8 kcal mol(-1), while R462Q reduces the activation energy by about 2.9 kcal mol(-1). Consistent with the active site model calculated using density functional theory, our results can support that the positive charge on R462 guanidino side chain group plays a negative role in the catalysis. Finally, the functional role of R462 was proposed to facilitate the formation of initial enzyme-substrate complex, but not in the subsequent catalytic degradation reaction. Graphical Abstract Degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.
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Affiliation(s)
- Fengxue Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China
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