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Shahri MA, Shirmast P, Ghafoori SM, Forwood JK. Deciphering the structure of a multi-drug resistant Acinetobacter baumannii short-chain dehydrogenase reductase. PLoS One 2024; 19:e0297751. [PMID: 38394109 PMCID: PMC10889901 DOI: 10.1371/journal.pone.0297751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
The rapidly increasing threat of multi-drug-resistant Acinetobacter baumannii infections globally, encompassing a range of clinical manifestations from skin and soft tissue infections to life-threatening conditions like meningitis and pneumonia, underscores an urgent need for novel therapeutic strategies. These infections, prevalent in both hospital and community settings, present a formidable challenge to the healthcare system due to the bacterium's widespread nature and dwindling effective treatment options. Against this backdrop, the exploration of bacterial short-chain dehydrogenase reductases (SDRs) emerges as a promising avenue. These enzymes play pivotal roles in various critical bacterial processes, including fatty acid synthesis, homeostasis, metabolism, and contributing to drug resistance mechanisms. In this study, we present the first examination of the X-ray crystallographic structure of an uncharacterized SDR enzyme from A. baumannii. The tertiary structure of this SDR is distinguished by a central parallel β-sheet, consisting of seven strands, which is flanked by eight α-helices. This configuration exhibits structural parallels with other enzymes in the SDR family, underscoring a conserved architectural theme within this enzyme class. Despite the current ambiguity regarding the enzyme's natural substrate, the importance of many SDR enzymes as targets in anti-bacterial agent design is well-established. Therefore, the detailed structural insights provided in this study open new pathways for the in-silico design of therapeutic agents. By offering a structural blueprint, our findings may provide a platform for future research aimed at developing targeted treatments against this and other multi-drug-resistant infections.
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Affiliation(s)
- Mahdi Abedinzadeh Shahri
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Paniz Shirmast
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Jade Kenneth Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
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2
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Kumar R, Das J, Mahto JK, Sharma M, Vivek S, Kumar P, Sharma AK. Crystal structure and molecular characterization of NADP +-farnesol dehydrogenase from cotton bollworm, Helicoverpaarmigera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 147:103812. [PMID: 35820537 DOI: 10.1016/j.ibmb.2022.103812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Farnesol dehydrogenase (FDL) orchestrates the oxidation reaction catalyzing farnesol to farnesal, a key step in the juvenile hormone (JH) biosynthesis pathway of insects and hence, represents a lucrative target for developing insect growth regulators (IGRs). However, information on the structural and functional characterization of JH-specific farnesol dehydrogenase in insects remains elusive. Herein, we identified a transcript that encodes farnesol dehydrogenase (HaFDL) from Helicoverpa armigera, a major pest of cotton. The investigations of molecular assembly, biochemical analysis and spatio-temporal expression profiling showed that HaFDL exists as a soluble homo-tetrameric form, exhibits a broad substrate affinity and is involved in the JH-specific farnesol oxidation in H. armigera. Additionally, the study presents the first crystal structure of the HaFDL-NADP enzyme complex determined at 1.6 Å resolution. Structural analysis revealed that HaFDL belongs to the NADP-specific cP2 subfamily of the classical short-chain dehydrogenase/reductase (SDR) family and exhibits typical structural features of those enzymes including the conserved nucleotide-binding Rossman-fold. The isothermal titration calorimetry (ITC) showed a high binding affinity (dissociation constant, Kd, 3.43 μM) of NADP to the enzyme. Comparative structural analysis showed a distinct substrate-binding pocket (SBP) loop with a spacious and hydrophobic substrate-binding pocket in HaFDL, consistent with the biochemically observed promiscuous substrate specificity. Finally, based on the crystal structure, substrate modeling and structural comparison with homologs, a two-step reaction mechanism is proposed. Overall, the findings significantly impact and contribute to our understanding of farnesol dehydrogenase functional properties in JH biosynthesis in H. armigera.
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Affiliation(s)
- Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India; ICAR-Central Institute for Cotton Research, Nagpur, India
| | - Joy Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India; ICAR-Central Institute for Cotton Research, Nagpur, India
| | - Jai Krishna Mahto
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Monica Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Shah Vivek
- ICAR-Central Institute for Cotton Research, Nagpur, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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3
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Li J, Dinh T, Phillips R. The crystal structure of the S154Y mutant carbonyl reductase from Leifsonia xyli explains enhanced activity for 3,5-Bis(trifluoromethyl)acetophenone reduction. Arch Biochem Biophys 2022; 720:109158. [PMID: 35247363 DOI: 10.1016/j.abb.2022.109158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022]
Abstract
Carbonyl reductase from Leifsonia xyli (LXCAR, UniProtKB - T2FLN4) can stereoselectively catalyze the reduction of 3,5-bis(trifluoromethyl)acetophenone (BTAP) to its corresponding alcohol, (R)-[3,5-bis(trifluoromethyl)phenyl]ethanol ((R)-BTPE), which is a valuable chiral intermediate for the synthesis of antiemetic drugs, Aprepitant and Fosaprepitant. Moreover, this protein was found to have a broad spectrum of substrate specificity and can asymmetrically catalyze the reduction of a variety of ketones and keto esters. Even though molecular modelling of this protein was done by Wang et al. (2014), a crystal structure has not yet obtained. In this study, a single mutant, S154Y, which was shown to have higher catalytic activity toward BTAP than that of the wild type, was overexpressed in Escherichia coli BL21 (DE3), purified, and crystallized. The crystal structure of LXCAR-S154Y explains how the mutant enzyme can work with BTAP more efficiently than wild type carbonyl reductase. Furthermore, the structure explains why LXCAR-S154Y can use either NADH or NADPH efficiently as a cofactor, as well as elucidates a proton relay system present in the enzyme.
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Affiliation(s)
- Jun Li
- School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, PR China.
| | - Tung Dinh
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
| | - Robert Phillips
- Department of Chemistry and of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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4
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Structural and functional investigation of AerF, a NADPH-dependent alkenal double bond reductase participating in the biosynthesis of Choi moiety of aeruginosin. J Struct Biol 2019; 209:107415. [PMID: 31726097 DOI: 10.1016/j.jsb.2019.107415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 10/27/2019] [Accepted: 11/08/2019] [Indexed: 01/16/2023]
Abstract
The 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety is an essential residue for the antithrombotic activities of aeruginosins, which are a class of cyanobacterial derived bioactive linear tetrapeptides. Biosynthetic pathway of Choi is still elusive. AerF was suggested to be involved in the biosynthesis of Choi, and can be assigned to the short-chain dehydrogenase/reductase (SDR) superfamily. However, both the exact role and the catalytic mechanism of AerF have not been elucidated. In this study, functional and mechanistic analyses of AerF from Microcystis aeruginosa were performed. Observation of enzymatic assay demonstrates that AerF is a NADPH-dependent alkenal double bond reductase that catalyzes the reduction of dihydro-4-hydroxyphenylpyruvate (H2HPP) to generate tetrahydro-4-hydroxyphenylpyruvate (H4HPP), which is the third step of the biosynthetic pathway from prephenate to Choi. Comparative structural analysis indicates that ligand binding-induced conformational change of AerF is different from that of the other SDR superfamily reductase using H2HPP as a substrate. Analyses of NADPH and substrate analogue binding sites combined with the results of mutagenesis analyses suggest that a particular serine residue mainly involves in the initiation of the proton transfer between the substrate and the residues of AerF, which is an uncommon feature in SDR superfamily reductase. Furthermore, based on the observations of structural and mutagenesis analyses, the catalytic mechanism of AerF is proposed and a proton transfer pathway in AerF is deduced.
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5
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Gräff M, Buchholz PC, Stockinger P, Bommarius B, Bommarius AS, Pleiss J. The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family. Proteins 2019; 87:443-451. [DOI: 10.1002/prot.25666] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Maike Gräff
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Patrick C.F. Buchholz
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
| | - Bettina Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Andreas S. Bommarius
- Department of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta Georgia
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of Stuttgart Stuttgart Germany
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6
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Wang P, Cao HY, Chen XL, Li CY, Li PY, Zhang XY, Qin QL, Todd JD, Zhang YZ. Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate-catabolizing bacteria. Mol Microbiol 2017; 105:674-688. [PMID: 28598523 DOI: 10.1111/mmi.13727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 12/24/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl-CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate-CoA ligase (PrpE) and acryloyl-CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP-catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl-CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.
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Affiliation(s)
- Peng Wang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Hai-Yan Cao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ping-Yi Li
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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7
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Selvaraj C, Krishnasamy G, Jagtap SS, Patel SK, Dhiman SS, Kim TS, Singh SK, Lee JK. Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Tanokura M, Miyakawa T, Guan L, Hou F. Structural analysis of enzymes used for bioindustry and bioremediation. Biosci Biotechnol Biochem 2015; 79:1391-401. [DOI: 10.1080/09168451.2015.1052770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abstract
Microbial enzymes have been widely applied in the large-scale, bioindustrial manufacture of food products and pharmaceuticals due to their high substrate specificity and stereoselectivity, and their effectiveness under mild conditions with low environmental burden. At the same time, bioremedial techniques using microbial enzymes have been developed to solve the problem of industrial waste, particularly with respect to persistent chemicals and toxic substances. And finally, structural studies of these enzymes have revealed the mechanistic basis of enzymatic reactions, including the stereoselectivity and binding specificity of substrates and cofactors. The obtained structural insights are useful not only to deepen our understanding of enzymes with potential bioindustrial and/or bioremedial application, but also for the functional improvement of enzymes through rational protein engineering. This review shows the structural bases for various types of enzymatic reactions, including the substrate specificity accompanying cofactor-controlled and kinetic mechanisms.
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Affiliation(s)
- Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Lijun Guan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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9
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Ding R, Xu C, Chen X, Bao M, Qiu X. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF from Microcystis aeruginosa, a putative reductase participating in aeruginosin biosynthesis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:466-70. [PMID: 25849511 DOI: 10.1107/s2053230x15005063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/12/2015] [Indexed: 11/10/2022]
Abstract
The 2-carboxy-6-hydroxyoctahydroindole moiety is an essential residue for the antithrombotic activity of aeruginosins, which are a class of cyanobacteria-derived bioactive linear tetrapeptides. The biosynthetic pathway of the 2-carboxy-6-hydroxyoctahydroindole moiety has not yet been resolved. AerF was indicated to be involved in the biosynthesis of the 2-carboxy-6-hydroxyoctahydroindole moiety. This study reports the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AerF from Microcystis aeruginosa with a C-terminal His6 tag. The crystal diffracted to a maximum resolution of 1.38 Å and belonged to the tetragonal space group P4322, with unit-cell parameters a = b = 101.581, c = 116.094 Å. The calculated Matthews coefficient and solvent content of the crystal were 2.47 Å(3) Da(-1) and 50.32%, respectively. The initial model of the structure was obtained by the molecular-replacement method and refinement of the structure is in progress.
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Affiliation(s)
- Ruyi Ding
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Cui Xu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Xu Chen
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Mengyun Bao
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
| | - Xiaoting Qiu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, People's Republic of China
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10
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Crystal structures and functional studies clarify substrate selectivity and catalytic residues for the unique orphan enzyme N-acetyl-D-mannosamine dehydrogenase. Biochem J 2014; 462:499-511. [PMID: 24969681 DOI: 10.1042/bj20140266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NAMDH (N-acetyl-D-mannosamine dehydrogenase), from the soil bacteroidete Flavobacterium sp. 141-8, catalyses a rare NAD+-dependent oxidation of ManNAc (N-acetyl-D-mannosamine) into N-acetylmannosamino-lactone, which spontaneously hydrolyses into N-acetylmannosaminic acid. NAMDH belongs to the SDR (short-chain dehydrogenase/reductase) superfamily and is the only NAMDH characterized to date. Thorough functional, stability, site-directed mutagenesis and crystallographic studies have been carried out to understand better the structural and biochemical aspects of this unique enzyme. NAMDH exhibited a remarkable alkaline pH optimum (pH 9.4) with a high thermal stability in glycine buffer (Tm=64°C) and a strict selectivity towards ManNAc and NAD+. Crystal structures of ligand-free and ManNAc- and NAD+-bound enzyme forms revealed a compact homotetramer having point 222 symmetry, formed by subunits presenting the characteristic SDR α3β7α3 sandwich fold. A highly developed C-terminal tail used as a latch connecting nearby subunits stabilizes the tetramer. A dense network of polar interactions with the substrate including the encasement of its acetamido group in a specific binding pocket and the hydrogen binding of the sugar 4OH atom ensure specificity for ManNAc. The NAMDH-substrate complexes and site-directed mutagenesis studies identify the catalytic tetrad and provide useful traits for identifying new NAMDH sequences.
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11
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Hou F, Miyakawa T, Kataoka M, Takeshita D, Kumashiro S, Uzura A, Urano N, Nagata K, Shimizu S, Tanokura M. Structural basis for high substrate-binding affinity and enantioselectivity of 3-quinuclidinone reductase AtQR. Biochem Biophys Res Commun 2014; 446:911-5. [PMID: 24642255 DOI: 10.1016/j.bbrc.2014.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 03/09/2014] [Indexed: 11/28/2022]
Abstract
(R)-3-Quinuclidinol, a useful compound for the synthesis of various pharmaceuticals, can be enantioselectively produced from 3-quinuclidinone by 3-quinuclidinone reductase. Recently, a novel NADH-dependent 3-quinuclidionone reductase (AtQR) was isolated from Agrobacterium tumefaciens, and showed much higher substrate-binding affinity (>100 fold) than the reported 3-quinuclidionone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of AtQR at 1.72 Å. Three NADH-bound protomers and one NADH-free protomer form a tetrameric structure in an asymmetric unit of crystals. NADH not only acts as a proton donor, but also contributes to the stability of the α7 helix. This helix is a unique and functionally significant part of AtQR and is related to form a deep catalytic cavity. AtQR has all three catalytic residues of the short-chain dehydrogenases/reductases family and the hydrophobic wall for the enantioselective reduction of 3-quinuclidinone as well as RrQR. An additional residue on the α7 helix, Glu197, exists near the active site of AtQR. This acidic residue is considered to form a direct interaction with the amine part of 3-quinuclidinone, which contributes to substrate orientation and enhancement of substrate-binding affinity. Mutational analyses also support that Glu197 is an indispensable residue for the activity.
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Affiliation(s)
- Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Michihiko Kataoka
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 559-8531, Japan; Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daijiro Takeshita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shoko Kumashiro
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Atsuko Uzura
- Research & Development Center, Nagase & Co., Ltd., 2-2-3 Muratani, Nishi-ku, Kobe 651-2241, Japan
| | - Nobuyuki Urano
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 559-8531, Japan; Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan; Faculty of Bioenvironmental Science, Kyoto Gakuen University, Sogabe-cho, Kameoka 621-8555, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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12
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Takeshita D, Kataoka M, Miyakawa T, Miyazono KI, Kumashiro S, Nagai T, Urano N, Uzura A, Nagata K, Shimizu S, Tanokura M. Structural basis of stereospecific reduction by quinuclidinone reductase. AMB Express 2014; 4:6. [PMID: 24507746 PMCID: PMC3922912 DOI: 10.1186/2191-0855-4-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 12/28/2013] [Indexed: 11/10/2022] Open
Abstract
Chiral molecule (R)-3-quinuclidinol, a valuable compound for the production of various pharmaceuticals, is efficiently synthesized from 3-quinuclidinone by using NADPH-dependent 3-quinuclidinone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of RrQR and the structure-based mutational analysis. The enzyme forms a tetramer, in which the core of each protomer exhibits the α/β Rossmann fold and contains one molecule of NADPH, whereas the characteristic substructures of a small lobe and a variable loop are localized around the substrate-binding site. Modeling and mutation analyses of the catalytic site indicated that the hydrophobicity of two residues, I167 and F212, determines the substrate-binding orientation as well as the substrate-binding affinity. Our results revealed that the characteristic substrate-binding pocket composed of hydrophobic amino acid residues ensures substrate docking for the stereospecific reaction of RrQR in spite of its loose interaction with the substrate.
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13
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Nishioka T, Yasutake Y, Nishiya Y, Tamura T. Structure-guided mutagenesis for the improvement of substrate specificity ofBacillus megateriumglucose 1-dehydrogenase IV. FEBS J 2012; 279:3264-75. [DOI: 10.1111/j.1742-4658.2012.08713.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Bezsudnova EY, Boyko KM, Polyakov KM, Dorovatovskiy PV, Stekhanova TN, Gumerov VM, Ravin NV, Skryabin KG, Kovalchuk MV, Popov VO. Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus. Biochimie 2012; 94:2628-38. [PMID: 22885278 DOI: 10.1016/j.biochi.2012.07.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/27/2012] [Indexed: 02/04/2023]
Abstract
Biochemical analysis of enantioselective short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus (TsAdh319) revealed unique polyextremophilic properties of the enzyme - half-life of 1 h at 100 °C, tolerance to high salt (up to 4 M) and organic solvents (50% v/v) concentrations. To elucidate the molecular basis of TsAdh319 polyextremophilicity, we determined the crystal structure of the enzyme in a binary complex with 5-hydroxy-NADP at 1.68 Å resolution. TsAdh319 has a tetrameric structure both in the crystals and in solution with an intersubunit disulfide bond. The substrate-binding pocket is hydrophobic, spacious and open that is consistent with the observed promiscuity in substrate specificity of TsAdh319. The present study revealed an extraordinary number of charged residues on the surface of TsAdh319, 70% of which were involved in ion pair interactions. Further we compared the structure of TsAdh319 with the structures of other homologous short-chain dehydrogenases/reductases (SDRs) from thermophilic and mesophilic organisms. We found that TsAdh319 has the highest arginine and aspartate + glutamate contents compared to the counterparts. The frequency of occurrence of salt bridges on the surface of TsAdh319 is the highest among the SDRs under consideration. No differences in the proline, tryptophan, and phenylalanine contents are observed; the compactness of the protein core of TsAdh319, the monomer and tetramer organization do not differ from that of the counterparts. We suggest that the unique thermostability of TsAdh319 is associated with the rigidity and simultaneous "resilience" of the structure provided by a compact hydrophobic core and a large number of surface ion pairs. An extensive salt bridge network also might maintain the structural integrity of TsAdh319 in high salinity.
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Affiliation(s)
- Ekaterina Y Bezsudnova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Pr. 33, Moscow 119071, Russia.
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Wuxiuer Y, Morgunova E, Cols N, Popov A, Karshikoff A, Sylte I, Gonzàlez-Duarte R, Ladenstein R, Winberg JO. An intact eight-membered water chain in drosophilid alcohol dehydrogenases is essential for optimal enzyme activity. FEBS J 2012; 279:2940-56. [PMID: 22741949 DOI: 10.1111/j.1742-4658.2012.08675.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All drosophilid alcohol dehydrogenases contain an eight-member water chain connecting the active site with the solvent at the dimer interface. A similar water chain has also been shown to exist in other short-chain dehydrogenase/reductase (SDR) enzymes, including therapeutically important SDRs. The role of this water chain in the enzymatic reaction is unknown, but it has been proposed to be involved in a proton relay system. In the present study, a connecting link in the water chain was removed by mutating Thr114 to Val114 in Scaptodrosophila lebanonensis alcohol dehydrogenase (SlADH). This threonine is conserved in all drosophilid alcohol dehydrogenases but not in other SDRs. X-ray crystallography of the SlADH(T114V) mutant revealed a broken water chain, the overall 3D structure of the binary enzyme-NAD(+) complex was almost identical to the wild-type enzyme (SlADH(wt) ). As for the SlADH(wt) , steady-state kinetic studies revealed that catalysis by the SlADH(T114V) mutant was consistent with a compulsory ordered reaction mechanism where the co-enzyme binds to the free enzyme. The mutation caused a reduction of the k(on) velocity for NAD(+) and its binding strength to the enzyme, as well as the rate of hydride transfer (k) in the ternary enzyme-NAD(+) -alcohol complex. Furthermore, it increased the pK(a) value of the group in the binary enzyme-NAD(+) complex that regulates the k(on) velocity of alcohol and alcohol-competitive inhibitors. Overall, the results indicate that an intact water chain is essential for optimal enzyme activity and participates in a proton relay system during catalysis.
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Affiliation(s)
- Yimingjiang Wuxiuer
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
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