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Beech JL, Fecko JA, Yennawar N, DuBois JL. Functional and spectroscopic approaches to determining thermal limitations of Rieske oxygenases. Methods Enzymol 2024; 703:299-328. [PMID: 39261001 DOI: 10.1016/bs.mie.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
The biotechnological potential of Rieske Oxygenases (ROs) and their cognate reductases remains unmet, in part because these systems can be functionally short-lived. Here, we describe a set of experiments aimed at identifying both the functional and structural stability limitations of ROs, using terephthalate (TPA) dioxygenase (from Comamonas strain E6) as a model system. Successful expression and purification of a cofactor-complete, histidine-tagged TPA dioxygenase and reductase protein system requires induction with the Escherichia coli host at stationary phase as well as a chaperone inducing cold-shock and supplementation with additional iron, sulfur, and flavin. The relative stability of the Rieske cluster and mononuclear iron center can then be assessed using spectroscopic and functional measurements following dialysis in an iron chelating buffer. These experiments involve measurements of the overall lifetime of the system via total turnover number using both UV-Visible absorbance and HPLC analyses, as well specific activity as a function of temperature. Important methods for assessing the stability of these multi-cofactor, multi-protein dependent systems at multiple levels of structure (secondary to quaternary) include differential scanning calorimetry, circular dichroism, and metallospectroscopy. Results can be rationalized in terms of three-dimensional structures and bioinformatics. The experiments described here provide a roadmap to a detailed characterization of the limitations of ROs. With a few notable exceptions, these issues are not widely addressed in current literature.
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Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Julia Ann Fecko
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Neela Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.
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2
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Tian J, Liu J, Knapp M, Donnan PH, Boggs DG, Bridwell-Rabb J. Custom tuning of Rieske oxygenase reactivity. Nat Commun 2023; 14:5858. [PMID: 37730711 PMCID: PMC10511449 DOI: 10.1038/s41467-023-41428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianxin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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Tian J, Garcia AA, Donnan PH, Bridwell-Rabb J. Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM. Biochemistry 2023. [PMID: 37188334 DOI: 10.1021/acs.biochem.3c00150] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Rieske nonheme iron oxygenases use two metallocenters, a Rieske-type [2Fe-2S] cluster and a mononuclear iron center, to catalyze oxidation reactions on a broad range of substrates. These enzymes are widely used by microorganisms to degrade environmental pollutants and to build complexity in a myriad of biosynthetic pathways that are industrially interesting. However, despite the value of this chemistry, there is a dearth of understanding regarding the structure-function relationships in this enzyme class, which limits our ability to rationally redesign, optimize, and ultimately exploit the chemistry of these enzymes. Therefore, in this work, by leveraging a combination of available structural information and state-of-the-art protein modeling tools, we show that three "hotspot" regions can be targeted to alter the site selectivity, substrate preference, and substrate scope of the Rieske oxygenase p-toluenesulfonate methyl monooxygenase (TsaM). Through mutation of six to 10 residues distributed between three protein regions, TsaM was engineered to behave as either vanillate monooxygenase (VanA) or dicamba monooxygenase (DdmC). This engineering feat means that TsaM was rationally engineered to catalyze an oxidation reaction at the meta and ortho positions of an aromatic substrate, rather than its favored native para position, and that TsaM was redesigned to perform chemistry on dicamba, a substrate that is not natively accepted by the enzyme. This work thus contributes to unlocking our understanding of structure-function relationships in the Rieske oxygenase enzyme class and expands foundational principles for future engineering of these metalloenzymes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Engineering Rieske oxygenase activity one piece at a time. Curr Opin Chem Biol 2023; 72:102227. [PMID: 36410250 PMCID: PMC9939785 DOI: 10.1016/j.cbpa.2022.102227] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Enzyme engineering plays a central role in the development of biocatalysts for biotechnology, chemical and pharmaceutical manufacturing, and environmental remediation. Rational design of proteins has historically relied on targeting active site residues to confer a protein with desirable catalytic properties. However, additional "hotspots" are also known to exist beyond the active site. Structural elements such as subunit-subunit interactions, entrance tunnels, and flexible loops influence enzyme catalysis and serve as potential "hotspots" for engineering. For the Rieske oxygenases, which use a Rieske cluster and mononuclear iron center to catalyze a challenging set of reactions, these outside of the active site regions are increasingly being shown to drive catalytic outcomes. Therefore, here, we highlight recent work on structurally characterized Rieske oxygenases that implicates architectural pieces inside and outside of the active site as key dictators of catalysis, and we suggest that these features may warrant attention in efforts aimed at Rieske oxygenase engineering.
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5
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Liu J, Knapp M, Jo M, Dill Z, Bridwell-Rabb J. Rieske Oxygenase Catalyzed C-H Bond Functionalization Reactions in Chlorophyll b Biosynthesis. ACS CENTRAL SCIENCE 2022; 8:1393-1403. [PMID: 36313167 PMCID: PMC9615114 DOI: 10.1021/acscentsci.2c00058] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Rieske oxygenases perform precise C-H bond functionalization reactions in anabolic and catabolic pathways. These reactions are typically characterized as monooxygenation or dioxygenation reactions, but other divergent reactions are also catalyzed by Rieske oxygenases. Chlorophyll(ide) a oxygenase (CAO), for example is proposed to catalyze two monooxygenation reactions to transform a methyl-group into the formyl-group of Chlorophyll b. This formyl group, like the formyl groups found in other chlorophyll pigments, tunes the absorption spectra of chlorophyllb and supports the ability of several photosynthetic organisms to adapt to environmental light. Despite the importance of this reaction, CAO has never been studied in vitro with purified protein, leaving many open questions regarding whether CAO can facilitate both oxygenation reactions using just the Rieske oxygenase machinery. In this study, we demonstrated that four CAO homologues in partnership with a non-native reductase convert a Chlorophyll a precursor, chlorophyllidea, into chlorophyllideb in vitro. Analysis of this reaction confirmed the existence of the proposed intermediate, highlighted the stereospecificity of the reaction, and revealed the potential of CAO as a tool for synthesizing custom-tuned natural and unnatural chlorophyll pigments. This work thus adds to our fundamental understanding of chlorophyll biosynthesis and Rieske oxygenase chemistry.
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6
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Design principles for site-selective hydroxylation by a Rieske oxygenase. Nat Commun 2022; 13:255. [PMID: 35017498 PMCID: PMC8752792 DOI: 10.1038/s41467-021-27822-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/15/2021] [Indexed: 01/12/2023] Open
Abstract
Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts. SxtT and GxtA are Rieske oxygenases that are involved in paralytic shellfish toxin biosynthesis and catalyze monohydroxylation reactions at different positions on the toxin scaffold. Here, the authors present crystal structures of SxtT and GxtA with the native substrates β-saxitoxinol and saxitoxin as well as a Xenon-pressurized structure of GxtA, which reveal a substrate access tunnel to the active site. Through structure-based mutagenesis studies the authors identify six residues in three different protein regions that determine the substrate specificity and site selectivity of SxtT and GxtA. These findings will aid the rational engineering of other Rieske oxygenases.
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Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK. Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 2019; 431:3647-3661. [PMID: 31412262 DOI: 10.1016/j.jmb.2019.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 01/06/2023]
Abstract
Caffeine, found in many foods, beverages, and pharmaceuticals, is the most used chemical compound for mental alertness. It is originally a natural product of plants and exists widely in environmental soil. Some bacteria, such as Pseudomonas putida CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes (NdmA, NdmB, NdmC, NdmD, and NdmE). The environmentally friendly enzymatic reaction products, methylxanthines, are high-value biochemicals that are used in the pharmaceutical and cosmetic industries. However, the structures and biochemical properties of bacterial N-demethylases remain largely unknown. Here, we report the structures of NdmA and NdmB, the initial N1- and N3-specific demethylases, respectively. Reverse-oriented substrate bindings were observed in the substrate-complexed structures, offering methyl position specificity for proper N-demethylation. For efficient sequential degradation of caffeine, these enzymes form a unique heterocomplex with 3:3 stoichiometry, which was confirmed by enzymatic assays, fluorescent labeling, and small-angle x-ray scattering. The binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state, was also determined to better understand electron transport during N-demethylation. These findings broaden our understanding of the caffeine degradation mechanism by bacterial enzymes and will enable their use for industrial applications.
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Affiliation(s)
- Jun Hoe Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Bong Heon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Shelby Brooks
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Seung Yeon Kang
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
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8
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Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K. Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:375-382. [PMID: 30910528 DOI: 10.1016/j.bbabio.2019.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
The alternative oxidase (AOX) is a monotopic diiron carboxylate protein which catalyzes the four-electron reduction of dioxygen to water by ubiquinol. Although we have recently determined the crystal structure of Trypanosoma brucei AOX (TAO) in the presence and absence of ascofuranone (AF) derivatives (which are potent mixed type inhibitors) the mechanism by which ubiquinol and dioxygen binds to TAO remain inconclusive. In this article, ferulenol was identified as the first competitive inhibitor of AOX which has been used to probe the binding of ubiquinol. Surface plasmon resonance reveals that AF is a quasi-irreversible inhibitor of TAO whilst ferulenol binding is completely reversible. The structure of the TAO-ferulenol complex, determined at 2.7 Å, provided insights into ubiquinol binding and has also identified a potential dioxygen molecule bound in a side-on conformation to the diiron center for the first time.
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Affiliation(s)
- Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan.
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan.
| | - Gen Takahashi
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Chiaki Tsuge
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Yasutoshi Kido
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Parasitology, Graduate School of Medicine, Osaka City University, Abeno-ku, Asahimachi 1-4-3, Osaka 545-8585, Japan
| | - Luke Young
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Satoshi Ueda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria 2222, Nigeria
| | - Takeshi Nara
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Bunkyo-ku, Hongo 2-1-1, Tokyo, 113-8421, Japan
| | - Teruki Honma
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyamacho-Minami 4, Tottori 680-8552, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Anthony L Moore
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
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Ferraro DJ, Okerlund A, Brown E, Ramaswamy S. One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. IUCRJ 2017; 4:648-656. [PMID: 28989720 PMCID: PMC5619856 DOI: 10.1107/s2052252517008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.
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Affiliation(s)
- Daniel J. Ferraro
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Adam Okerlund
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Brown
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - S. Ramaswamy
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- TAS, Institute for Stem Cell Biology and Regenerative Medicine, GKVK POST, Bangalore 560 065, India
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Penfield JS, Worrall LJ, Strynadka NC, Eltis LD. Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases. J Biol Chem 2014; 289:25523-36. [PMID: 25049233 DOI: 10.1074/jbc.m114.575886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.
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Affiliation(s)
| | - Liam J Worrall
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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