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Pi S, Luo Y, Liu YJ. Thorough Understanding of Bioluminophore Production in Bacterial Bioluminescence. J Phys Chem A 2022; 126:6604-6616. [DOI: 10.1021/acs.jpca.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuangqi Pi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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2
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Silverstein TP. How enzymes harness highly unfavorable proton transfer reactions. Protein Sci 2021; 30:735-744. [PMID: 33554401 DOI: 10.1002/pro.4037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/12/2022]
Abstract
Acid-base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate isomerase, a glutamate side chain (nominal pKa ≈ 4 in solution) can in fact deprotonate a CH group that is vicinal to a carbonyl (pKa ≈ 18 in solution). This is true because of three distinct interactions: (a) ground state pKa shifts due to environment polarity and electrostatics; (b) dramatic increases in effective molarity due to optimization of proximity and orientation; and (c) transition state pKa shifts due to binding interactions and the formation of strong low barrier hydrogen bonds. In this report, we review the literature showing that the sum of these three effects supplies more than enough free energy to push forward proton transfer reactions that under standard conditions are exceedingly nonspontaneous and slow.
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3
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Furuhata Y, Kato Y. Asymmetric Roles of Two Histidine Residues in Streptococcus pyogenes Cas9 Catalytic Domains upon Chemical Rescue. Biochemistry 2021; 60:194-200. [PMID: 33428390 DOI: 10.1021/acs.biochem.0c00766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
CRISPR-Cas9 technology has been at the forefront of the field of biology. The Streptococcus pyogenes (SpyCas9) protein forms a complex with guide RNA and can recognize and cleave double-stranded DNA through hybridization based on 20 base pairings. SpyCas9 has two nuclease domains, HNH and RuvC, each of which cuts each DNA strand, and both contain critical histidine residues. Although previously reported crystal structures provide useful geometric information, the extent to which these residues functionally contribute to catalysis is unknown. Here, we mutated histidine residues on HNH and RuvC domains to alanine or glycine and attempted to rescue the enzymatic activity by adding the imidazole molecule, using an in vitro DNA cleavage assay. H840A and H840G exhibited rescued enzymatic activity on the HNH domain following imidazole addition, suggesting that H840 acts as a general base. We also tested various chemicals and found that the pKa of imidazole derivatives, and not their molecular shape, correlated with the rescue effect. In contrast, both H983A and H983G on the RuvC domain did not exhibit a rescue effect following imidazole addition. Our chemical rescue approach will provide crucial insight into understanding Cas9 catalysis, complementing structural analyses.
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Affiliation(s)
- Yuichi Furuhata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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4
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Tinikul R, Lawan N, Akeratchatapan N, Pimviriyakul P, Chinantuya W, Suadee C, Sucharitakul J, Chenprakhon P, Ballou DP, Entsch B, Chaiyen P. Protonation status and control mechanism of flavin-oxygen intermediates in the reaction of bacterial luciferase. FEBS J 2020; 288:3246-3260. [PMID: 33289305 DOI: 10.1111/febs.15653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/15/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Bacterial luciferase catalyzes a bioluminescent reaction by oxidizing long-chain aldehydes to acids using reduced FMN and oxygen as co-substrates. Although a flavin C4a-peroxide anion is postulated to be the intermediate reacting with aldehyde prior to light liberation, no clear identification of the protonation status of this intermediate has been reported. Here, transient kinetics, pH variation, and site-directed mutagenesis were employed to probe the protonation state of the flavin C4a-hydroperoxide in bacterial luciferase. The first observed intermediate, with a λmax of 385 nm, transformed to an intermediate with a λmax of 375 nm. Spectra of the first observed intermediate were pH-dependent, with a λmax of 385 nm at pH < 8.5 and 375 at pH > 9, correlating with a pKa of 7.7-8.1. These data are consistent with the first observed flavin C4a intermediate at pH < 8.5 being the protonated flavin C4a-hydroperoxide, which loses a proton to become an active flavin C4a-peroxide. Stopped-flow studies of His44Ala, His44Asp, and His44Asn variants showed only a single intermediate with a λmax of 385 nm at all pH values, and none of these variants generate light. These data indicate that His44 variants only form a flavin C4a-hydroperoxide, but not an active flavin C4a-peroxide, indicating an essential role for His44 in deprotonating the flavin C4a-hydroperoxide and initiating chemical catalysis. We also investigated the function of the adjacent His45; stopped-flow data and molecular dynamics simulations identify the role of this residue in binding reduced FMN.
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Affiliation(s)
- Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiangmai University, Thailand
| | - Nattanon Akeratchatapan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wachirawit Chinantuya
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chutintorn Suadee
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand
| | - David P Ballou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Barrie Entsch
- School of Science and Technology, University of New England, Armidale, NSW, Australia
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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5
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Abstract
Bacterial luciferase is a flavin-dependent monooxygenase which is remarkable for its distinctive feature in transforming chemical energy to photons of visible light. The bacterial luciferase catalyzes bioluminescent reaction using reduced flavin mononucleotide, long-chain aldehyde and oxygen to yield oxidized flavin, corresponding acid, water and light at λmax around 490nm. The enzyme comprises of two non-identical α and β subunits, where α subunit is a catalytic center and β subunit is crucially required for maintaining catalytic function of the α subunit. The crystal structure with FMN bound and mutagenesis studies have assigned a number of amino acid residues that are important in coordinating critical reactions and stabilizing intermediates to attain optimum reaction efficiency. The enzyme achieves monooxygenation by generating C4a-hydroperoxyflavin intermediate that later changes its protonation status to become C4a-peroxyflavin, which is necessary for the nucleophilic attacking with aldehyde substrate. The decomposing of C4a-peroxyhemiacetal produces excited C4a-hydroxyflavin and acid product. The chemical basis regrading bioluminophore generation in Lux reaction remains an inconclusive issue. However, current data can, at least, demonstrate the involvement of electron transfer to create radical molecules which is the key step in this mechanism. Lux is a self-sufficient bioluminescent system in which all substrates can be recycled and produced by a group of enzymes from the lux operon. This makes Lux distinctively advantageous over other luciferases for reporter enzyme application. The progression of understanding of Lux catalysis is beneficial to improve light emitting efficiency in order to expand the robustness of Lux application.
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Kotlobay AA, Kaskova ZM, Yampolsky IV. Palette of Luciferases: Natural Biotools for New Applications in Biomedicine. Acta Naturae 2020. [DOI: 10.32607/actanaturae.11152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Optoanalytical methods based on using genetically encoded bioluminescent enzymes,luciferases, allow one to obtain highly sensitive signals, are non-invasive, and require no external irradiation. Bioluminescence is based on the chemical reaction of oxidation of a low-molecular-weight substrate (luciferin) by atmospheric oxygen, which is catalyzed by an enzyme (luciferase). Relaxation of the luciferin oxidation product from its excited state is accompanied by a release of a quantum of light, which can be detected as an analytical signal.The ability to express luciferase genes in various heterological systems and high quantum yields of luminescence reactions have made these tools rather popular in biology and medicine. Amongseveral naturally available luciferases, a few have been found to be useful for practicalapplication. Luciferase size, the wavelength of its luminescence maximum, enzyme thermostability, optimal pH of the reaction, and the need for cofactors areparameters that may differ for luciferases from different groups of organisms, and this fact directly affects the choice of the application area for each enzyme. It is quite important to overview the whole range of currently available luciferases based ontheir biochemical properties before choosing one bioluminescent probe suitable for a specific application.
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Kotlobay AA, Kaskova ZM, Yampolsky IV. Palette of Luciferases: Natural Biotools for New Applications in Biomedicine. Acta Naturae 2020; 12:15-27. [PMID: 32742724 PMCID: PMC7385095 DOI: 10.32607/actanaturae.10967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 12/30/2022] Open
Abstract
Optoanalytical methods based on using genetically encoded bioluminescent enzymes, luciferases, allow one to obtain highly sensitive signals, are non-invasive, and require no external irradiation. Bioluminescence is based on the chemical reaction of oxidation of a low-molecular-weight substrate (luciferin) by atmospheric oxygen, which is catalyzed by an enzyme (luciferase). Relaxation of the luciferin oxidation product from its excited state is accompanied by a release of a quantum of light, which can be detected as an analytical signal. The ability to express luciferase genes in various heterological systems and high quantum yields of luminescence reactions have made these tools rather popular in biology and medicine. Among several naturally available luciferases, a few have been found to be useful for practical application. Luciferase size, the wavelength of its luminescence maximum, enzyme thermostability, optimal pH of the reaction, and the need for cofactors are parameters that may differ for luciferases from different groups of organisms, and this fact directly affects the choice of the application area for each enzyme. It is quite important to overview the whole range of currently available luciferases based on their biochemical properties before choosing one bioluminescent probe suitable for a specific application.
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Affiliation(s)
- A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Z. M. Kaskova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - I. V. Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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8
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Lee J, Müller F, Visser AJWG. The Sensitized Bioluminescence Mechanism of Bacterial Luciferase. Photochem Photobiol 2018; 95:679-704. [PMID: 30485901 DOI: 10.1111/php.13063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/17/2018] [Indexed: 11/27/2022]
Abstract
After more than one-half century of investigations, the mechanism of bioluminescence from the FMNH2 assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase-bound FMNH-OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.
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Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | | | - Antonie J W G Visser
- Laboratory of Biochemistry Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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9
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Luo Y, Liu YJ. Revisiting the Origin of Bacterial Bioluminescence: QM/MM Study on Oxygenation Reaction of Reduced Flavin in Protein. Chemphyschem 2018; 20:405-409. [PMID: 30417568 DOI: 10.1002/cphc.201800970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/07/2018] [Indexed: 12/18/2022]
Abstract
Bacterial bioluminescence is initiated by the oxygenation reaction of reduced flavin mononucleotide in luciferase. This enzymatic oxygenation occurs in a wide range of biological processes including cellular redox metabolism, biocatalysis, biosynthesis and homeostasis. However, little is known about the mechanism of the enzymatic reaction between singlet reduced flavin and triplet oxygen. To explore the enigmatic oxygenation, for the first time, the reaction of reduced flavin anion with oxygen was studied in bacterial luciferase by a combined quantum mechanics and molecular mechanics method as well as molecular dynamics simulation. The calculated results demonstrate that the reaction proceeds via a proton-coupled electron transfer (PCET) pathway, and the essential αHis44 acts as a catalytic acid to provide the proton. The currently proposed PCET mechanism clearly describes the initial steps of bacterial bioluminescence, and could be suitable for the other flavin oxygenation reactions in enzymes.
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Affiliation(s)
- Yanling Luo
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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10
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Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. J Am Chem Soc 2017; 139:11089-11095. [PMID: 28719738 DOI: 10.1021/jacs.7b03547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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11
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Lamba V, Yabukarski F, Pinney M, Herschlag D. Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:9902-9. [PMID: 27410422 DOI: 10.1021/jacs.6b04796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Proton transfer reactions are ubiquitous in enzymes and utilize active site residues as general acids and bases. Crystal structures and site-directed mutagenesis are routinely used to identify these residues, but assessment of their catalytic contribution remains a major challenge. In principle, effective molarity measurements, in which exogenous acids/bases rescue the reaction in mutants lacking these residues, can estimate these catalytic contributions. However, these exogenous moieties can be restricted in reactivity by steric hindrance or enhanced by binding interactions with nearby residues, thereby resulting in over- or underestimation of the catalytic contribution, respectively. With these challenges in mind, we investigated the catalytic contribution of an aspartate general base in ketosteroid isomerase (KSI) by exogenous rescue. In addition to removing the general base, we systematically mutated nearby residues and probed each mutant with a series of carboxylate bases of similar pKa but varying size. Our results underscore the need for extensive and multifaceted variation to assess and minimize steric and positioning effects and determine effective molarities that estimate catalytic contributions. We obtained consensus effective molarities of ∼5 × 10(4) M for KSI from Comamonas testosteroni (tKSI) and ∼10(3) M for KSI from Pseudomonas putida (pKSI). An X-ray crystal structure of a tKSI general base mutant showed no additional structural rearrangements, and double mutant cycles revealed similar contributions from an oxyanion hole mutation in the wild-type and base-rescued reactions, providing no indication of mutational effects extending beyond the general base site. Thus, the high effective molarities suggest a large catalytic contribution associated with the general base. A significant portion of this effect presumably arises from positioning of the base, but its large magnitude suggests the involvement of additional catalytic mechanisms as well.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Margaux Pinney
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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12
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Deeva AA, Temlyakova EA, Sorokin AA, Nemtseva EV, Kratasyuk VA. Structural distinctions of fast and slow bacterial luciferases revealed by phylogenetic analysis. Bioinformatics 2016; 32:3053-3057. [DOI: 10.1093/bioinformatics/btw386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 11/14/2022] Open
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13
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Armacost K, Musila J, Gathiaka S, Ellis HR, Acevedo O. Exploring the Catalytic Mechanism of Alkanesulfonate Monooxygenase Using Molecular Dynamics. Biochemistry 2014; 53:3308-17. [DOI: 10.1021/bi5002085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kira Armacost
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Jonathan Musila
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Symon Gathiaka
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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14
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Structure, Mechanism, and Mutation of Bacterial Luciferase. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 154:47-74. [DOI: 10.1007/10_2014_281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Identification of critical steps governing the two-component alkanesulfonate monooxygenase catalytic mechanism. Biochemistry 2012; 51:6378-87. [PMID: 22775358 DOI: 10.1021/bi300138d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alkanesulfonate monooxygenase enzyme (SsuD) catalyzes the oxygenolytic cleavage of a carbon-sulfur bond from sulfonated substrates. A mechanism involving acid-base catalysis has been proposed for the desulfonation mechanism by SsuD. In the proposed mechanism, base catalysis is involved in abstracting a proton from the alkane peroxyflavin intermediate, while acid catalysis is needed for the protonation of the FMNO(-) intermediate. The pH profiles of k(cat) indicate that catalysis by SsuD requires a group with a pK(a) of 6.6 ± 0.2 to be deprotonated and a second group with a pK(a) of 9.5 ± 0.1 to be protonated. The upper pK(a) value was not present in the pH profiles of k(cat)/K(m). Several conserved amino acid residues (His228, His11, His333, Cys54, and Arg226) have been identified as having potential catalytic importance due to the similar spatial arrangements with close structural and functional relatives of SsuD. Substitutions to these amino acid residues were generated, and the pH dependencies were evaluated and compared to wild-type SsuD. Although a histidine residue was previously proposed to be the active site base, the His variants possessed similar steady-state kinetic parameters as wild-type SsuD. Interestingly, R226A and R226K SsuD variants possessed undetectable activity, and there was no detectable formation of the C4a-(hydro)peroxyflavin intermediate for the Arg226 SsuD variants. Guanidinium rescue with the R226A SsuD variant resulted in the recovery of 1.5% of the wild-type SsuD k(cat) value. These results implicate Arg226 playing a critical role in catalysis and provide essential insights into the mechanistic steps that guide the SsuD desulfonation process.
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16
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Moon AF, Midon M, Meiss G, Pingoud A, London RE, Pedersen LC. Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae. Nucleic Acids Res 2010; 39:2943-53. [PMID: 21113026 PMCID: PMC3074123 DOI: 10.1093/nar/gkq1152] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
EndA is a sequence non-specific endonuclease that serves as a virulence factor during Streptococcus pneumoniae infection. Expression of EndA provides a strategy for evasion of the host's neutrophil extracellular traps, digesting the DNA scaffold structure and allowing further invasion by S. pneumoniae. To define mechanisms of catalysis and substrate binding, we solved the structure of EndA at 1.75 Å resolution. The EndA structure reveals a DRGH (Asp-Arg-Gly-His) motif-containing ββα-metal finger catalytic core augmented by an interesting ‘finger-loop’ interruption of the active site α-helix. Subsequently, we delineated DNA binding versus catalytic functionality using structure-based alanine substitution mutagenesis. Three mutants, H154A, Q186A and Q192A, exhibited decreased nuclease activity that appears to be independent of substrate binding. Glu205 was found to be crucial for catalysis, while residues Arg127/Lys128 and Arg209/Lys210 contribute to substrate binding. The results presented here provide the molecular foundation for development of specific antibiotic inhibitors for EndA.
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Affiliation(s)
- Andrea F Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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17
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Ellis HR. The FMN-dependent two-component monooxygenase systems. Arch Biochem Biophys 2010; 497:1-12. [PMID: 20193654 DOI: 10.1016/j.abb.2010.02.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/13/2010] [Accepted: 02/16/2010] [Indexed: 11/19/2022]
Abstract
The FMN-dependent two-component monooxygenase systems catalyze a diverse range of reactions. These two-component systems are composed of an FMN reductase enzyme and a monooxygenase enzyme that catalyze the oxidation of various substrates. The role of the reductase is to supply reduced flavin to the monooxygenase enzyme, while the monooxygenase enzyme utilizes the reduced flavin to activate molecular oxygen. Unlike flavoproteins with a tightly or covalently bound prosthetic group, these enzymes catalyze the reductive and oxidative half-reaction on two separate enzymes. An interesting feature of these enzymes is their ability to transfer reduced flavin from the reductase to the monooxygenase enzyme. This review covers the reported mechanistic and structural properties of these enzyme systems, and evaluates the mechanism of flavin transfer.
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Affiliation(s)
- Holly R Ellis
- The Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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18
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Catalytic role of a conserved cysteine residue in the desulfonation reaction by the alkanesulfonate monooxygenase enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:97-105. [DOI: 10.1016/j.bbapap.2009.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 09/08/2009] [Accepted: 09/11/2009] [Indexed: 11/19/2022]
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19
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Zhan X, Carpenter RA, Ellis HR. Catalytic Importance of the Substrate Binding Order for the FMNH2-Dependent Alkanesulfonate Monooxygenase Enzyme. Biochemistry 2008; 47:2221-30. [DOI: 10.1021/bi701853w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xuanzhi Zhan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Russell A. Carpenter
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Holly R. Ellis
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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Viviani VR, Ohmiya Y. Bioluminescence Color Determinants of Phrixothrix Railroad-worm Luciferases: Chimeric Luciferases, Site-directed Mutagenesis of Arg 215 and Guanidine effect¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720267bcdopr2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Ling J, Roy H, Ibba M. Mechanism of tRNA-dependent editing in translational quality control. Proc Natl Acad Sci U S A 2006; 104:72-7. [PMID: 17185419 PMCID: PMC1765480 DOI: 10.1073/pnas.0606272104] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein synthesis requires the pairing of amino acids with tRNAs catalyzed by the aminoacyl-tRNA synthetases. The synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. The fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from tRNAs before they are delivered to the ribosome. Although editing has been described in numerous synthetases, the reaction mechanism is unknown. To define the mechanism of editing, phenylalanyl-tRNA synthetase was used to investigate different models for hydrolysis of the noncognate product Tyr-tRNA(Phe). Deprotonation of a water molecule by the highly conserved residue betaHis-265, as proposed for threonyl-tRNA synthetase, was excluded because replacement of this and neighboring residues had little effect on editing activity. Model building suggested that, instead of directly catalyzing hydrolysis, the role of the editing site is to discriminate and properly position noncognate substrate for nucleophilic attack by water. In agreement with this model, replacement of certain editing site residues abolished substrate specificity but only reduced the catalytic efficiency of hydrolysis 2- to 10-fold. In contrast, substitution of the 3'-OH group of tRNA(Phe) severely impaired editing and revealed an essential function for this group in hydrolysis. The phenylalanyl-tRNA synthetase editing mechanism is also applicable to threonyl-tRNA synthetase and provides a paradigm for synthetase editing.
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Affiliation(s)
| | - Hervé Roy
- Department of Microbiology, Ohio State University, Columbus, OH 43210
| | - Michael Ibba
- *Biochemistry Program and
- Department of Microbiology, Ohio State University, Columbus, OH 43210
- To whom correspondence should be addressed at:
Department of Microbiology, Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210-1292. E-mail:
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22
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Chen WJ, Lai PJ, Lai YS, Huang PT, Lin CC, Liao TH. Probing the catalytic mechanism of bovine pancreatic deoxyribonuclease I by chemical rescue. Biochem Biophys Res Commun 2006; 352:689-96. [PMID: 17141190 DOI: 10.1016/j.bbrc.2006.11.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 11/15/2006] [Indexed: 10/23/2022]
Abstract
Previous structural and mutational studies of bovine pancreatic deoxyribonuclease I (bpDNase I) have demonstrated that the active site His134 and His252 played critical roles in catalysis. In our present study, mutations of these two His residues to Gln, Ala or Gly reduced the DNase activity by a factor of four to five orders of magnitude. When imidazole or primary amines were added exogenously to the Ala or Gly mutants, the residual DNase activities were substantially increased by 60-120-fold. The rescue with imidazole was pH- and concentration-dependent. The pH-activity profiles showed nearly bell-shaped curves, with the maximum activity enhancement for H134A at pH 6.0 and that for H252A at pH 7.5. These findings indicated that the protonated form of imidazole was responsible for the rescue in H134A, and the unprotonated form was for that in H252A, prompting us to assign unambiguously the roles for His134 as a general acid, and His252 as a general base, in bpDNase I catalysis.
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Affiliation(s)
- Wei-Jung Chen
- Institute of Biotechnology, College of Bioresources, National Ilan University, Ilan 26047, Taiwan.
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23
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Perrotta AT, Wadkins TS, Been MD. Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme. RNA (NEW YORK, N.Y.) 2006; 12:1282-91. [PMID: 16690998 PMCID: PMC1484427 DOI: 10.1261/rna.14106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In the ribozyme from the hepatitis delta virus (HDV) genomic strand RNA, a cytosine side chain is proposed to facilitate proton transfer in the transition state of the reaction and, thus, act as a general acid-base catalyst. Mutation of this active-site cytosine (C75) reduced RNA cleavage rates by as much as one million-fold, but addition of exogenous cytosine and certain nucleobase or imidazole analogs can partially rescue activity in these mutants. However, pH-rate profiles for the rescued reactions were bell shaped, and only one leg of the pH-rate curve could be attributed to ionization of the exogenous nucleobase or buffer. When a second potential ionizable nucleobase (C41) was removed, one leg of the bell-shaped curve was eliminated in the chemical-rescue reaction. With this construct, the apparent pK(a) determined from the pH-rate profile correlated with the solution pK(a) of the buffer, and the contribution of the buffer to the rate enhancement could be directly evaluated in a free-energy or Brønsted plot. The free-energy relationship between the acid dissociation constant of the buffer and the rate constant for cleavage (Brønsted value, beta, = approximately 0.5) was consistent with a mechanism in which the buffer acted as a general acid-base catalyst. These data support the hypothesis that cytosine 75, in the intact ribozyme, acts as a general acid-base catalyst.
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Affiliation(s)
- Anne T Perrotta
- Department of Biochemistry, Duke University Medical School, Durham, NC 27710, USA
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24
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Li CH, Tu SC. Probing the Functionalities of αGlu328 and αAla74 of Vibrio harveyi Luciferase by Site-Directed Mutagenesis and Chemical Rescue. Biochemistry 2005; 44:13866-73. [PMID: 16229475 DOI: 10.1021/bi051182i] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work aimed at identifying essential residues on the alpha subunit of Vibrio harveyi luciferase and elucidating their functional roles. Four conserved alpha-subunit residues at the proposed luciferase active site were initially mutated to Ala. Screening of the in vivo bioluminescence of cells expressing these mutated luciferases allowed the work to focus on alphaGlu328 for additional mutations to Phe, Leu, Gln, His, and Asp. V. harveyi luciferase is known to contain, at the same proposed active site, an unusual cis-peptide linkage between alphaAla74 and alphaAla75. To explore the structure-function relationship, luciferase variants alphaA74F and alphaA74G were constructed. The six alphaGlu328-mutated and the two alphaAla74-mutated luciferase variants were purified and characterized with respect to Vmax, Michaelis constants, light and dark decays, quantum yield, and, for alphaE328F and alphaA74F, yield of the 4a-hydroperoxyFMN intermediate and the ability to oxidize aldehyde substrate. Results indicated that the structural integrities of both alphaGlu328 and alphaAla74 were essential to luciferase bioluminescence activity. Moreover, the essentiality of alphaGlu328 was linked to the acidic nature of its side chain. The low activity of alphaE328A was sensitive to chemical rescue by sodium acetate, an effect that was not reproduced by phosphate. The efficiency of activity rescue by acetate progressively increased at lower pH in the range from 6.0 to 8.0, supporting the interpretation of alphaGlu328 as a catalytic general acid. The rescuing effect of acetate was on a reaction step after the formation of the 4a-hydroperoxyFMN intermediate. The exact catalytic function of alphaGlu328 is unclear, but possibilities are discussed.
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Affiliation(s)
- Chi-Hui Li
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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25
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Aufhammer SW, Warkentin E, Ermler U, Hagemeier CH, Thauer RK, Shima S. Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family. Protein Sci 2005; 14:1840-9. [PMID: 15937276 PMCID: PMC2253363 DOI: 10.1110/ps.041289805] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 03/22/2005] [Accepted: 03/25/2005] [Indexed: 10/25/2022]
Abstract
Methylenetetratetrahydromethanopterin reductase (Mer) is involved in CO(2) reduction to methane in methanogenic archaea and catalyses the reversible reduction of methylenetetrahydromethanopterin (methylene-H(4)MPT) to methyl-H(4)MPT with coenzyme F(420)H(2), which is a reduced 5'-deazaflavin. Mer was recently established as a TIM barrel structure containing a nonprolyl cis-peptide bond but the binding site of the substrates remained elusive. We report here on the crystal structure of Mer in complex with F(420) at 2.6 A resolution. The isoalloxazine ring is present in a pronounced butterfly conformation, being induced from the Re-face of F(420) by a bulge that contains the non-prolyl cis-peptide bond. The bindingmode of F(420) is very similar to that in F(420)-dependent alcohol dehydrogenase Adf despite the low sequence identity of 21%. Moreover, binding of F(420) to the apoenzyme was only associated with minor conformational changes of the polypeptide chain. These findings allowed us to build an improved model of FMN into its binding site in bacterial luciferase, which belongs to the same structural family as Mer and Adf and also contains a nonprolyl cis-peptide bond in an equivalent position.
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Venkataraman P, Lamb RA, Pinto LH. Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. J Biol Chem 2005; 280:21463-72. [PMID: 15784624 DOI: 10.1074/jbc.m412406200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influenza virus M2 proton-selective ion channel activity facilitates virus uncoating, a process that occurs in the acidic environment of the endosome. The M2 channel causes acidification of the interior of the virus particle, which results in viral protein-protein dissociation. The M2 protein is a homotetramer that contains in its aqueous pore a histidine residue (His-37) that acts as a selectivity filter and a tryptophan residue (Trp-41) that acts as a channel gate. Substitution of His-37 modifies M2 ion channel properties drastically. However, the results of such experiments are difficult to interpret because substitution of His-37 could cause gross structural changes to the channel pore. We described here experiments in which partial or, in some cases, full rescue of specific M2 ion channel properties of His-37 substitution mutants was achieved by addition of imidazole to the bathing medium. Chemical rescue was demonstrated for three histidine substitution mutant ion channels (M2-H37G, M2-H37S, and M2-H37T) and for two double mutants in which the Trp-41 channel gate was also mutated (H37G/W41Y and H37G/W41A). Currents of the M2-H37G mutant ion channel were inhibited by Cu(II), which has been shown to coordinate with His-37 in the wild-type channel. Chemical rescue was very specific for imidazole. Buffer molecules that were neutral when protonated (4-morpholineethanesulfonic acid and 3-morpholino-2-hydroxypropanesulfonic acid) did not rescue ion channel activity of the M2-H37G mutant ion channel, but 1-methylimidazole did provide partial rescue of function. These results were consistent with a model for proton transport through the pore of the wild-type channel in which the imidazole side chain of His-37 acted as an intermediate proton acceptor/donor group.
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Affiliation(s)
- Padmavati Venkataraman
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois 60208-3500, USA
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27
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Sciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, Malatesta F, Schimperna G, Savino C, Vallone B. The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis. EMBO J 2003; 22:205-15. [PMID: 12514126 PMCID: PMC140106 DOI: 10.1093/emboj/cdg031] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ActVA-Orf6 monooxygenase from Streptomyces coelicolor that catalyses the oxidation of an aromatic intermediate of the actinorhodin biosynthetic pathway is a member of a class of small monooxygenases that carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The overall structure is a ferredoxin-like fold with a novel dimeric assembly, indicating that the widely represented ferredoxin fold may sustain yet another functionality. The resolution (1.3 A) of the enzyme structure and its complex with substrate and product analogues allows us to visualize the mechanism of binding and activation of the substrate for attack by molecular oxygen, and utilization of two gates for the reaction components including a proton gate and an O(2)/H(2)O gate with a putative protein channel. This is the first crystal structure of an enzyme involved in the tailoring of a type II aromatic polyketide and illustrates some of the enzyme-substrate recognition features that may apply to a range of other enzymes involved in modifying a polyketide core structure.
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Affiliation(s)
- Giuliano Sciara
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Steven G. Kendrew
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Adriana E. Miele
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Neil G. Marsh
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Luca Federici
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Giuliana Schimperna
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Carmelinda Savino
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche and CNR, Centro di Studi sulla Biologia Molecolare, c/o Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, Piazzale A.Moro, 5, 00185 Roma, Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, 67100 L’Aquila, Istituto G.Donegani, 28100 Novara, Italy, Biotica Technology Ltd, 181A Huntingdon Road, Cambridge CB3 0DJ, UK and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA Corresponding author e-mail:
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28
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Wei CJ, Lei B, Tu SC. Characterization of the binding of Photobacterium phosphoreum P-flavin by Vibrio harveyi Luciferase. Arch Biochem Biophys 2001; 396:199-206. [PMID: 11747297 DOI: 10.1006/abbi.2001.2612] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The isolated Photobacterium phosphoreum luciferase is associated with a bound flavin designated P-flavin and tentatively identified as 6-(3"-myristic acid)-FMN. Since FMN and myristic acid are products of the normal luciferase reaction, we explored the possibility that P-flavin can also be bound by luciferase from other luminous bacteria and serve as an active site probe. P-flavin has never been detected in Vibrio harveyi cells. We found that the V. harveyi luciferase binds P. phosphoreum P-flavin, at a ratio of 1 P-flavin per luciferase alphabeta dimer, and with concomitant absorption spectral perturbation of P-flavin, fluorescence quenching of P-flavin and luciferase, and activity inhibition of luciferase. Isolated P-flavin can be fully reduced photochemically. V. harveyi luciferase bound the oxidized P-flavin with a K(d) (or K(i) competitively against decanal) of 0.1-0.16 microM, which is three orders of magnitude lower than the K(d) for FMN binding but similar to that of reduced FMN binding. The reduced P-flavin exhibited a K(i) (competitively against the reduced FMN substrate) of 0.16 microM, also similar to the K(d) for reduced FMN. Hence, the covalent attachment of myristic acid to FMN greatly and preferentially enhanced the binding of oxidized P-flavin. The dissociation of P-flavin was slow in comparison with the binding of reduced FMN and decanal substrates. Modification of the alphaCys106 near the active site by N-ethylmaleimide can be retarded by P-flavin. These findings indicate that P-flavin is potentially a superb active site probe for luciferase. We hypothesize that P-flavin is a by-product of luciferase generated by a side reaction which is trivial with the V. harveyi luciferase but significant in the P. phosphoreum luciferase-catalyzed reaction.
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Affiliation(s)
- C J Wei
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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29
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Abstract
Although mechanisms of metabolite channeling have been extensively studied, the nature of reduced flavin transfer from donor to acceptor enzymes remains essentially unexplored. In this review, identities and properties of reduced flavin-producing enzymes (namely flavin reductases) and reduced flavin-requiring processes and enzymes are summarized. By using flavin reductase-luciferase enzyme couples from luminous bacteria, two types of reduced flavin channeling were observed involving the differential transfers of the reduced flavin cofactor and the reduced flavin product of reductase to luciferase. The exact mode of transfer is controlled by the specific makeup of the constituent enzymes within the reductase-luciferase couple. The plausible physiological significance of the monomer-dimer equilibrium of the NADPH-specific flavin reductase from Vibrio harveyi is also discussed.
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Affiliation(s)
- S C Tu
- Department of Biology and Biochemistry, University of Houston, TX 77204-5513, USA.
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30
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Lin LY, Sulea T, Szittner R, Vassilyev V, Purisima EO, Meighen EA. Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data. Protein Sci 2001; 10:1563-71. [PMID: 11468353 PMCID: PMC2374094 DOI: 10.1110/ps.7201] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2001] [Revised: 05/04/2001] [Accepted: 05/04/2001] [Indexed: 10/16/2022]
Abstract
Although the crystal structure of Vibrio harveyi luciferase has been elucidated, the binding sites for the flavin mononucleotide and fatty aldehyde substrates are still unknown. The determined location of the phosphate-binding site close to Arg 107 on the alpha subunit of luciferase is supported here by point mutagenesis. This information, together with previous structure-activity data for the length of the linker connecting the phosphate group to the isoalloxazine ring represent important characteristics of the luciferase-bound conformation of the flavin mononucleotide. A model of the luciferase-flavin complex is developed here using flexible docking supplemented by these structural constraints. The location of the phosphate moiety was used as the anchor in a flexible docking procedure performed by conformation search by using the Monte Carlo minimization approach. The resulting databases of energy-ranked feasible conformations of the luciferase complexes with flavin mononucleotide, omega-phosphopentylflavin, omega-phosphobutylflavin, and omega-phosphopropylflavin were filtered according to the structure-activity profile of these analogs. A unique model was sought not only on energetic criteria but also on the geometric requirement that the isoalloxazine ring of the active flavin analogs must assume a common orientation in the luciferase-binding site, an orientation that is also inaccessible to the inactive flavin analog. The resulting model of the bacterial luciferase-flavin mononucleotide complex is consistent with the experimental data available in the literature. Specifically, the isoalloxazine ring of the flavin mononucleotide interacts with the Ala 74-Ala 75 cis-peptide bond as well as with the Cys 106 side chain in the alpha subunit of luciferase. The model of the binary complex reveals a distinct cavity suitable for aldehyde binding adjacent to the isoalloxazine ring and flanked by other key residues (His 44 and Trp 250) implicated in the active site.
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Affiliation(s)
- L Y Lin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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31
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Lee HJ, Lloyd MD, Clifton IJ, Harlos K, Dubus A, Baldwin JE, Frere JM, Schofield CJ. Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase. The role of arginine 258. J Biol Chem 2001; 276:18290-5. [PMID: 11279000 DOI: 10.1074/jbc.m100085200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deacetoxycephalosporin C synthase is an iron(II) 2-oxoglutaratedependent oxygenase that catalyzes the oxidative ring-expansion of penicillin N to deacetoxycephalosporin C. The wild-type enzyme is only able to efficiently utilize 2-oxoglutarate and 2-oxoadipate as a 2-oxoacid co-substrate. Mutation of arginine 258, the side chain of which forms an electrostatic interaction with the 5-carboxylate of the 2-oxoglutarate co-substrate, to a glutamine residue reduced activity to about 5% of the wild-type enzyme with 2-oxoglutarate. However, other aliphatic 2-oxoacids, which were not co-substrates for the wild-type enzyme, were utilized by the R258Q mutant. These 2-oxoacids "rescued" catalytic activity to the level observed for the wild-type enzyme as judged by penicillin N and G conversion. These co-substrates underwent oxidative decarboxylation as observed for 2-oxoglutarate in the normal reaction with the wild-type enzyme. Crystal structures of the iron(II)- 2-oxo-3-methylbutanoate (1.5 A), and iron(II)-2-oxo-4-methylpentanoate (1.6 A) enzyme complexes were obtained, which reveal the molecular basis for this "chemical co-substrate rescue" and help to rationalize the co-substrate selectivity of 2-oxoglutaratedependent oxygenases.
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Affiliation(s)
- H J Lee
- Oxford Centre for Molecular Sciences and the Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QY, United Kingdom
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32
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Shih IH, Been MD. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc Natl Acad Sci U S A 2001; 98:1489-94. [PMID: 11171978 PMCID: PMC29284 DOI: 10.1073/pnas.98.4.1489] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76 Delta) ribozymes in D(2)O and H(2)O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76 Delta mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under k(cat)/K(M) conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (beta) of 0.51 was determined for the base-rescued reaction of C76 Delta. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage.
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Affiliation(s)
- I H Shih
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Fischer F, Fetzner S. Site-directed mutagenesis of potential catalytic residues in 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase, and hypothesis on the catalytic mechanism of 2,4-dioxygenolytic ring cleavage. FEMS Microbiol Lett 2000; 190:21-7. [PMID: 10981684 DOI: 10.1111/j.1574-6968.2000.tb09256.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
1H-3-Hydroxy-4-oxoquinoline 2,4-dioxygenase (Qdo) is a cofactor-free dioxygenase proposed to belong to the alpha/beta hydrolase fold superfamily of enzymes. Alpha/beta Hydrolases contain a highly conserved catalytic triad (nucleophile-acidic residue-histidine). We previously identified a corresponding catalytically essential histidine residue in Qdo. However, as shown by amino acid replacements through site-directed mutagenesis, nucleophilic and acidic residues of Qdo considered as possible triad residues were not absolutely required for activity. This suggests that Qdo does not contain the canonical catalytic triad of the alpha/beta hydrolase fold enzymes. Some radical trapping agents affected the Qdo-catalyzed reaction. A hypothetical mechanism of Qdo-catalyzed dioxygenation of 1H-3-hydroxy-4-oxoquinoline is compared with the dioxygenation of FMNH2 catalyzed by bacterial luciferase, which also uses a histidine residue as catalytic base.
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Affiliation(s)
- F Fischer
- AG Mikrobiologie, Carl von Ossietzky Universität Oldenburg, Germany
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34
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Viviani VR, Ohmiya Y. Bioluminescence color determinants of Phrixothrix railroad-worm luciferases: chimeric luciferases, site-directed mutagenesis of Arg 215 and guanidine effect. Photochem Photobiol 2000; 72:267-71. [PMID: 10946582 DOI: 10.1562/0031-8655(2000)072<0267:bcdopr>2.0.co;2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chimeric proteins were produced using the green light-emitting luciferase of Phrixothrix vivianii (PxGr: lambda max = 548 nm) and the red light-emitting luciferase of Phrixothrix hirtus (PxRe: lambda max = 623 nm). Constructs containing residues 1-344 of the red light-emitting luciferase with residues 345-545 of the green light emitting one emitted red light (PxReGr; lambda max = 613 nm), while the reverse emitted green light (PxGrRe; lambda max = 552 nm). From these results we conclude that the region 1-344 determines the color of bioluminescence (BL) in railroad-worm luciferases, and that residues above 344 are not involved. The substitution R215S in the green light-emitting luciferase (PxGr) resulted in a approximately 40 nm redshift on the BL spectrum (lambda max = 585 nm) and an associated decrease of activity, whereas the same mutation in PxRe luciferase had little effect. Guanidine was shown to cause blueshifts in the BL spectra and stimulate the activity of the red-emitting luciferases (from lambda max = 623 to lambda max = 600 nm) and in PxGr R215S (from lambda max = 585 to lambda max = 560 nm) mutant luciferase, but not in the green-emitting luciferases, suggesting that guanidine can simulate positively charged residues involved in BL color determination.
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Affiliation(s)
- V R Viviani
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA.
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35
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Jiang W, Locke G, Harpel MR, Copeland RA, Marcinkeviciene J. Role of lys100 in human dihydroorotate dehydrogenase: mutagenesis studies and chemical rescue by external amines. Biochemistry 2000; 39:7990-7. [PMID: 10891080 DOI: 10.1021/bi000630d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical modification, mutagenesis, chemical rescue, and isotope effect studies are used to identify and probe the roles of several conserved amino acid groups in catalysis by human dihydroorotate dehydrogenase. Time- and pH-dependent inactivation of human dihydroorotate dehydrogenase by trinitrobenzenesulfonate implicates at least one critical lysyl residue in catalysis. Of four highly conserved lysines, only the cognate of Lys255 was previously suggested to have catalytic functionality. We now show that replacement of either Lys184 or Lys186 by mutagenesis does not impact, whereas substitution of Lys100 abolishes, enzymatic activity. However, activity is partially restored to K100C (or K100A) by inclusion of exogenous primary amines in reaction mixtures. This rescued activity saturates with respect to numerous amines and exhibits a steric discrimination reflected in K(d,(amine)) values. For all amines, rescued k(cat) values were only approximately 10% of wild type and independent of amine basicity. K(M) values for dihydroorotate and coenzyme Q(0) were similar to wild type. Thus, exogenous amines (as surrogates for Lys100) apparently complement a chemical, not binding, step(s) of catalysis, which does not entail proton transfer. In support of this postulate, solvent kinetic isotope effect analysis indicates that Lys100 stabilizes developing negative charge on the isoalloxazine ring of flavin mononucleotide during hydride transfer, as has been observed for a number of flavoprotein oxidoreductases. Ser215 of human dihydroarotate dehydrogenase (DHODase) was also studied because of its alignment with the putative active-site base Cys130 of Lactococcus lactisDHODase. Substantial retention of activity by S215C, yet complete loss of activity for S215A, is consistent with Ser215 serving as the active-site base in the human enzyme.
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Affiliation(s)
- W Jiang
- Department of Chemical Enzymology, DuPont Pharmaceuticals Company, P. O. Box 80400, Wilmington, Delaware 19880-0400, USA
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36
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Dmitriev LF. Bacterial luminescence: luminescence mechanism with cyclic peroxide participation and dependence on reactive oxygen species (a hypothesis). Biochimie 2000; 82:237-44. [PMID: 10863007 DOI: 10.1016/s0300-9084(00)00211-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Chemically initiated exchange (CIEE) luminescence reactions were reviewed and a new mechanism of luminescence with peracid as an intermediate is proposed; bacterial luminescence is generally considered to be a case of dioxetane luminescence, or, to be more precise, CIEE-luminescence which includes the generation of a cyclic peroxide. In the hypothesis the monooxygenase reaction (aldehyde -->fatty acid) should not be coupled with emitter generation as is usually believed, but only with the generation of peracid. As to the generation of the emitter, excited flavin, it is likely to occur later, during the interaction of flavin with cyclic peroxide. Its consequence is the breaking of two chemical bonds (O-O and C-C) in the cyclic peroxide and simultaneous generation of 4alpha-hydroxyflavin in exited state. In general, the generation of light includes three stages: 1) the monooxygenase reaction and the concurrent production of peracid; 2) the conversion of peracid to cyclic peroxide; and 3) the interaction of cyclic peroxide with flavin (through the CIEE mechanism).
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Affiliation(s)
- L F Dmitriev
- Department of Microbiology, School of Biology, Lomonosov Moscow State University, Russia.
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37
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Abstract
Ribozymes use a number of the same catalytic strategies as protein enzymes. However, general base catalysis by a ribozyme has not been demonstrated. In the hepatitis delta virus antigenomic ribozyme, imidazole buffer rescued activity of a mutant with a cytosine-76 (C76) to uracil substitution. In addition, a C76 to adenine substitution reduced the apparent pKa (where Ka is the acid constant) of the self-cleavage reaction by an amount consistent with differences in the pKa values of these two side chains. These results suggest that, in the wild-type ribozyme, C76 acts as a general base. This finding has implications for potential catalytic functions of conserved cytosines and adenines in other ribozymes and in ribonuclear proteins with enzymatic activity.
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Affiliation(s)
- A T Perrotta
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, NC 27710 USA
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38
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Abstract
There are presently several proposed catalytic mechanisms of yeast enolase, all of which have emerged from separate structural investigations of enolase from yeast and lobster muscle. However, the identities of the residues functioning as the general acid/base pair are not yet established unambiguously. In the Mn(2+)-phosphoglycolate complex of lobster muscle enolase, the imidazole group of His157 (His159 in the yeast enolase numbering system) is in van der Waals contact (4.5 A) with the C(2) of the inhibitor [Duquerroy et al. (1995) Biochemistry 34, 12513-12523]. To gain further information about the role played by His159 in the catalytic mechanism of yeast enolase this residue has been mutated to Ala. The gene encoding for the H159A mutation has been constructed and the mutant protein has been expressed in Escherichia coli. The purified mutant protein is folded properly as indicated by near- and far-UV circular dichroism and fluorescence data, and the mutation has no significant effect on the formation of ternary and quaternary enzyme-ligand complexes. In a typical assay, H159A showed 0.01% of wild-type specific activity, which corresponds to a reduction in k(cat) of 4 orders of magnitude. The H159A fails to ionize the C-2 proton of either 2-PGA or phosphoglycolate. These findings are consistent with His159 serving as a potential catalytic base in the enolase reaction. We have suggested that His159 could also serve as a metal ligand at the third, inhibitory, metal binding site. This proposal is consistent with the catalytic mechanism of yeast enolase. Binding of metal ion at site III interferes with His159 reacting as the catalytic base, i.e., abstracting the C(2) proton from 2-PGA. Metal binding studies support the above proposal. Mn(2+) binding at sites I and II for the His159Ala mutant is identical to that of wild type. The binding of Mn(2+) at the third, inhibitory site of H159A is a factor of 3 weaker compared to wild-type enolase. The factor of 3 in binding is reasonable for the contribution to binding strength of a single nondominant ligand in a chelate [Klemba, M., and Regan, L. (1995) Biochemistry 34, 10094-10100. Regan, L. (1993) Annu. Rev. Biophys. Biomol. Struct. 22, 257-281. Cha et al. (1994) J. Biol. Chem. 269, 2687-2694].
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Affiliation(s)
- D A Vinarov
- Department of Chemistry and Biochemistry, University of Notre Dame, Indiana 46556, USA
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39
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Lehoux IE, Mitra B. (S)-Mandelate dehydrogenase from Pseudomonas putida: mutations of the catalytic base histidine-274 and chemical rescue of activity. Biochemistry 1999; 38:9948-55. [PMID: 10433701 DOI: 10.1021/bi9907532] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(S)-Mandelate dehydrogenase from Pseudomonas putida, an FMN-dependent alpha-hydroxy acid dehydrogenase, oxidizes (S)-mandelate to benzoylformate. The generally accepted catalytic mechanism for this enzyme involves the formation of a carbanion intermediate. Histidine-274 has been proposed to be the active-site base that abstracts the substrate alpha-proton to generate the carbanion. Histidine-274 was altered to glycine, alanine, and asparagine. All three mutants were completely inactive. The mutants were able to form adducts with sulfite, though with much weaker affinity than the wild-type enzyme. Binding of the inhibitor, (R)-mandelate, was not greatly affected by the mutation, unlike that of the substrate, (S)-mandelate, indicating that H274 plays a role in substrate binding. The activity of H274G and, to a lesser extent, H274A could be partially restored by the addition of exogenous imidazoles. The maximum rescued activity for H274G with imidazole was approximately 0.1% of the wild-type value. Saturation kinetics obtained for rescued activity suggest that formation of a ternary complex of imidazole, enzyme, and substrate is required for catalysis. pH-dependence studies confirm that the free base form of imidazole is the rescue agent. An earlier study of pH profiles of the wild-type enzyme indicated that deprotonation of a residue with a pK(a) of 5.5 in the free enzyme was essential for activity (Lehoux, I. E., and Mitra, B. (1999) Biochemistry 38, 5836-5848). Data obtained in this work confirm that the pK(a) of 5.5 belongs to histidine-274.
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Affiliation(s)
- I E Lehoux
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
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Admiraal SJ, Schneider B, Meyer P, Janin J, Véron M, Deville-Bonne D, Herschlag D. Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase. Biochemistry 1999; 38:4701-11. [PMID: 10200157 DOI: 10.1021/bi9827565] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nonenzymatic reaction of ATP with a nucleophile to generate ADP and a phosphorylated product proceeds via a dissociative transition state with little bond formation to the nucleophile. Consideration of the dissociative nature of the nonenzymatic transition state leads to the following question: To what extent can the nucleophile be activated in enzymatic phosphoryl transfer? We have addressed this question for the NDP kinase reaction. A mutant form of the enzyme lacking the nucleophilic histidine (H122G) can be chemically rescued for ATP attack by imidazole or other exogenous small nucleophiles. The ATP reaction is 50-fold faster with the wild-type enzyme, which has an imidazole nucleophile positioned for reaction by a covalent bond, than with H122G, which employs a noncovalently bound imidazole nucleophile [(kcat/KM)ATP]. Further, a 4-fold advantage for imidazole positioned in the nucleophile binding pocket created by the mutation is suggested from comparison of the reaction of H122G and ATP with an imidazole versus a water nucleophile, after correction for the intrinsic reactivities of imidazole and water toward ATP in solution. X-ray structural analysis shows no detectable rearrangement of the residues surrounding His 122 upon mutation to Gly 122. The overall rate effect of approximately 10(2)-fold for the covalent imidazole nucleophile relative to water is therefore attributed to positioning of the nucleophile with respect to the reactive phosphoryl group. This is underscored by the more deleterious effect of replacing ATP with AlphaTauPgammaS in the wild-type reaction than in the imidazole-rescued mutant reaction, as follows. For the wild-type, AlphaTauPgammaS presumably disrupts positioning between nucleophile and substrate, resulting in a large thio effect of 300-fold, whereas precise alignment is already disrupted in the mutant because there is no covalent bond to the nucleophile, resulting in a smaller thio effect of 10-fold. In summary, the results suggest a catalytic role for activation of the nucleophile by positioning in phosphoryl transfer catalyzed by NDP kinase.
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Affiliation(s)
- S J Admiraal
- Department of Biochemistry, Beckman Center B400, Stanford University, Stanford, California 94305-5307, USA
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Li H, Ortego BC, Maillard KI, Willson RC, Tu SC. Effects of mutations of the alpha His45 residue of Vibrio harveyi luciferase on the yield and reactivity of the flavin peroxide intermediate. Biochemistry 1999; 38:4409-15. [PMID: 10194361 DOI: 10.1021/bi982396l] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work was undertaken to investigate the functional consequences of mutations of the essential alpha His45 residue of Vibrio harveyi luciferase, especially with respect to the yield and reactivity of the flavin 4a-hydroperoxide intermediate II. A total of 14 luciferase variants, each with a different single-residue replacement for the alpha His45, were examined. These variants showed changes, mostly slight, in their light decay rates of the nonturnover luminescence reaction and in their Km values for decanal and reduced riboflavin 5'-phosphate (FMNH2). All alpha His45 mutants, however, showed markedly reduced bioluminescence activities, the magnitude of the reduction ranging from about 300-fold to 6 orders of magnitude. Remarkably, a good correlation was obtained for the wild-type luciferase, 12 alpha His45-mutated luciferases, and six additional variants with mutations of other alpha-subunit histidine residues between the degrees of luminescence activity reduction and the dark decay rates of intermediate II. Such a correlation further indicates that the activation of the O-O bond fission is an important function of the flavin 4a-hydroperoxide intermediate II. Both alpha H45G and alpha H45W were found to bind near-stoichiometric amounts of FMNH2. Moreover, each variant catalyzed the oxidation of bound FMNH2 by two mechanisms, with a minor pathway leading to the formation of a luminescence-active intermediate II and a major dark pathway not involving any detectable flavin 4a-hydroperoxide species. This latter pathway mimics that in the normal catalysis by flavooxidases, and its elicitation in luciferase was demonstrated for the first time by single-residue mutations.
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Affiliation(s)
- H Li
- Department of Biology and Biochemistry, University of Houston, Texas 77204-5513, USA
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Watanabe A, Kurokawa Y, Yoshimura T, Kurihara T, Soda K, Esaki N, Watababe A. Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5'-phosphate. Chemical rescue studies of Lys39 --> Ala mutant. J Biol Chem 1999; 274:4189-94. [PMID: 9933615 DOI: 10.1074/jbc.274.7.4189] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lysine residue binding with the cofactor pyridoxal 5'-phosphate (PLP) plays an important role in catalysis, such as in the transaldimination and abstraction of alpha-hydrogen from a substrate amino acid in PLP-dependent enzymes. We studied the role of Lys39 of alanine racemase (EC 5.1.1.1) from Bacillus stearothermophilus, the PLP-binding residue of the enzyme, by replacing it site-specifically with alanine and characterizing the resultant K39A mutant enzyme. The mutant enzyme turned out to be inherently inactive, but gained an activity as high as about 0.1% of that of the wild-type enzyme upon addition of 0.2 M methylamine. The amine-assisted activity of the mutant enzyme depended on the pKa values and molecular volumes of the alkylamines used. A strong kinetic isotope effect was observed when alpha-deuterated D-alanine was used as a substrate in the methylamine-assisted reaction, but little effect was observed using its antipode. In marked contrast, only L-enantiomer of alanine showed a solvent isotope effect in deuterium oxide in the methylamine-assisted reaction. These results suggest that methylamine serves as a base not only to abstract the alpha-hydrogen from D-alanine but also to transfer a proton from water to the alpha-position of the deprotonated (achiral) intermediate to form D-alanine. Therefore, the exogenous amine can be regarded as a functional group fully representing Lys39 of the wild-type enzyme. Lys39 of the wild-type enzyme probably acts as the base catalyst specific to the D-enantiomer of alanine. Another residue specific to the L-enantiomer in the wild-type enzyme is kept intact in the K39A mutant.
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Affiliation(s)
- A Watanabe
- Laboratory of Biofunctional Molecules, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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