1
|
Wang PH, Nishikawa S, McGlynn SE, Fujishima K. One-Pot De Novo Synthesis of [4Fe-4S] Proteins Using a Recombinant SUF System under Aerobic Conditions. ACS Synth Biol 2023; 12:2887-2896. [PMID: 37467114 PMCID: PMC10594875 DOI: 10.1021/acssynbio.3c00155] [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: 03/15/2023] [Indexed: 07/21/2023]
Abstract
Fe-S clusters are essential cofactors mediating electron transfer in respiratory and metabolic networks. However, obtaining active [4Fe-4S] proteins with heterologous expression is challenging due to (i) the requirements for [4Fe-4S] cluster assembly, (ii) the O2 lability of [4Fe-4S] clusters, and (iii) copurification of undesired proteins (e.g., ferredoxins). Here, we established a facile and efficient protocol to express mature [4Fe-4S] proteins in the PURE system under aerobic conditions. An enzyme aconitase and thermophilic ferredoxin were selected as model [4Fe-4S] proteins for functional verification. We first reconstituted the SUF system in vitro via a stepwise manner using the recombinant SUF subunits (SufABCDSE) individually purified from E. coli. Later, the incorporation of recombinant SUF helper proteins into the PURE system enabled mRNA translation-coupled [4Fe-4S] cluster assembly under the O2-depleted conditions. To overcome the O2 lability of [4Fe-4S] Fe-S clusters, an O2-scavenging enzyme cascade was incorporated, which begins with formate oxidation by formate dehydrogenase for NADH regeneration. Later, NADH is consumed by flavin reductase for FADH2 regeneration. Finally, bifunctional flavin reductase, along with catalase, removes O2 from the reaction while supplying FADH2 to the SufBC2D complex. These amendments enabled a one-pot, two-step synthesis of mature [4Fe-4S] proteins under aerobic conditions, yielding holo-aconitase with a maximum concentration of ∼0.15 mg/mL. This renovated system greatly expands the potential of the PURE system, paving the way for the future reconstruction of redox-active synthetic cells and enhanced cell-free biocatalysis.
Collapse
Affiliation(s)
- Po-Hsiang Wang
- Department
of Chemical Engineering and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
- Graduate
Institute of Environmental Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Shota Nishikawa
- Earth-Life
Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- School
of Life Science and Technology, Tokyo Institute
of Technology, Tokyo 152-8550, Japan
| | - Shawn Erin McGlynn
- Earth-Life
Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue
Marble Space Institute of Science, Seattle, Washington 98154, United States
| | - Kosuke Fujishima
- Earth-Life
Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Graduate
School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| |
Collapse
|
2
|
Song Z, Wei C, Li C, Gao X, Mao S, Lu F, Qin HM. Customized exogenous ferredoxin functions as an efficient electron carrier. BIORESOUR BIOPROCESS 2021; 8:109. [PMID: 38650207 PMCID: PMC10992505 DOI: 10.1186/s40643-021-00464-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Ferredoxin (Fdx) is regarded as the main electron carrier in biological electron transfer and acts as an electron donor in metabolic pathways of many organisms. Here, we screened a self-sufficient P450-derived reductase PRF with promising production yield of 9OHAD (9α-hydroxy4-androstene-3,17-dione) from AD, and further proved the importance of [2Fe-2S] clusters of ferredoxin-oxidoreductase in transferring electrons in steroidal conversion. The results of truncated Fdx domain in all oxidoreductases and mutagenesis data elucidated the indispensable role of [2Fe-2S] clusters in the electron transfer process. By adding the independent plant-type Fdx to the reaction system, the AD (4-androstene-3,17-dione) conversion rate have been significantly improved. A novel efficient electron transfer pathway of PRF + Fdx + KshA (KshA, Rieske-type oxygenase of 3-ketosteroid-9-hydroxylase) in the reaction system rather than KshAB complex system was proposed based on analysis of protein-protein interactions and redox potential measurement. Adding free Fdx created a new conduit for electrons to travel from reductase to oxygenase. This electron transfer pathway provides new insight for the development of efficient exogenous Fdx as an electron carrier.
Collapse
Affiliation(s)
- Zhan Song
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Cancan Wei
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Chao Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xin Gao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
- National Engineering Laboratory for Industrial Enzymes, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| |
Collapse
|
3
|
Zhou J, Lénon M, Ravanat JL, Touati N, Velours C, Podskoczyj K, Leszczynska G, Fontecave M, Barras F, Golinelli-Pimpaneau B. Iron-sulfur biology invades tRNA modification: the case of U34 sulfuration. Nucleic Acids Res 2021; 49:3997-4007. [PMID: 33744947 PMCID: PMC8053098 DOI: 10.1093/nar/gkab138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Sulfuration of uridine 34 in the anticodon of tRNAs is conserved in the three domains of life, guaranteeing fidelity of protein translation. In eubacteria, it is catalyzed by MnmA-type enzymes, which were previously concluded not to depend on an iron-sulfur [Fe-S] cluster. However, we report here spectroscopic and iron/sulfur analysis, as well as in vitro catalytic assays and site-directed mutagenesis studies unambiguously showing that MnmA from Escherichia coli can bind a [4Fe-4S] cluster, which is essential for sulfuration of U34-tRNA. We propose that the cluster serves to bind and activate hydrosulfide for nucleophilic attack on the adenylated nucleoside. Intriguingly, we found that E. coli cells retain s2U34 biosynthesis in the ΔiscUA ΔsufABCDSE strain, lacking functional ISC and SUF [Fe-S] cluster assembly machineries, thus suggesting an original and yet undescribed way of maturation of MnmA. Moreover, we report genetic analysis showing the importance of MnmA for sustaining oxidative stress.
Collapse
Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Marine Lénon
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, UMR 5819, F-38000 Grenoble, France
| | - Nadia Touati
- IR CNRS Renard, Chimie-ParisTech, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| | - Frédéric Barras
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Universités, 11 Place Marcelin Berthelot, 75231 Paris cedex 05, France
| |
Collapse
|
4
|
Joo JC, Khusnutdinova AN, Flick R, Kim T, Bornscheuer UT, Yakunin AF, Mahadevan R. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chem Sci 2017; 8:1406-1413. [PMID: 28616142 PMCID: PMC5460604 DOI: 10.1039/c6sc02842j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/08/2016] [Indexed: 12/26/2022] Open
Abstract
Adipic acid, a precursor for Nylon-6,6 polymer, is one of the most important commodity chemicals, which is currently produced from petroleum. The biosynthesis of adipic acid from glucose still remains challenging due to the absence of biocatalysts required for the hydrogenation of unsaturated six-carbon dicarboxylic acids to adipic acid. Here, we demonstrate the first enzymatic hydrogenation of 2-hexenedioic acid and muconic acid to adipic acid using enoate reductases (ERs). ERs can hydrogenate 2-hexenedioic acid and muconic acid producing adipic acid with a high conversion rate and yield in vivo and in vitro. Purified ERs exhibit a broad substrate spectrum including aromatic and aliphatic 2-enoates and a significant oxygen tolerance. The discovery of the hydrogenation activity of ERs contributes to an understanding of the catalytic mechanism of these poorly characterized enzymes and enables the environmentally benign biosynthesis of adipic acid and other chemicals from renewable resources.
Collapse
Affiliation(s)
- Jeong Chan Joo
- Center for Bio-based Chemistry , Division of Convergence Chemistry , Korea Research Institute of Chemical Technology , 141 Gajeong-ro, Yuseong-gu , Daejeon 34114 , Republic of Korea .
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Taeho Kim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Uwe T Bornscheuer
- Institute of Biochemistry , Department of Biotechnology & Enzyme Catalysis , Greifswald University , Felix-Hausdorff-Strasse 4 , 17487 Greifswald , Germany
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , ON M5S 3E5 , Canada . ;
| |
Collapse
|
5
|
Cyanidioschyzon merolae
ferredoxin: A high resolution crystal structure analysis and its thermal stability. FEBS Lett 2011; 585:1299-302. [DOI: 10.1016/j.febslet.2011.03.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/07/2011] [Accepted: 03/09/2011] [Indexed: 11/23/2022]
|
6
|
Kondo T, Nomata J, Fujita Y, Itoh S. EPR study of 1Asp-3Cys ligated 4Fe-4S iron-sulfur cluster in NB-protein (BchN-BchB) of a dark-operative protochlorophyllide reductase complex. FEBS Lett 2010; 585:214-8. [PMID: 21126521 DOI: 10.1016/j.febslet.2010.11.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/23/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
Abstract
Dark-operative protochlorophyllide oxidoreductase, a nitrogenase-like enzyme, contains two [4Fe-4S] clusters, one in the L-protein ((BchL)(2)) and the other in the NB-protein ((BchN-BchB)(2)). The reduced NB-cluster in the NB-protein, which is ligated by 1Asp/3Cys residues, showed a broad S=3/2 electron paramagnetic resonance signal that is rather rare in [4Fe-4S] clusters. A 4Cys-ligated NB-cluster in the mutated variant BchB-D36C protein, in which the Asp36 was replaced by a Cys, gave a rhombic normal S=1/2 signal and lost the catalytic activity. The results suggest that Asp36 contributes to the low redox potential necessary to reduce protochlorophyllide.
Collapse
Affiliation(s)
- Toru Kondo
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan.
| | | | | | | |
Collapse
|
7
|
Gruner I, Frädrich C, Böttger LH, Trautwein AX, Jahn D, Härtig E. Aspartate 141 is the fourth ligand of the oxygen-sensing [4Fe-4S]2+ cluster of Bacillus subtilis transcriptional regulator Fnr. J Biol Chem 2010; 286:2017-21. [PMID: 21068385 DOI: 10.1074/jbc.m110.191940] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Bacillus subtilis redox regulator Fnr controls genes of the anaerobic metabolism in response to low oxygen tension. An unusual structure for the oxygen-sensing [4Fe-4S](2+) cluster was detected by a combination of genetic experiments with UV-visible and Mössbauer spectroscopy. Asp-141 was identified as the fourth iron-sulfur cluster ligand besides three Cys residues. Exchange of Asp-141 with Ala abolished functional in vivo complementation of an fnr knock-out strain by the mutagenized fnr gene and in vitro DNA binding of the recombinant regulator FnrD141A. In contrast, substitution of Asp-141 with Cys preserved [4Fe-4S](2+) structure and regulator function.
Collapse
Affiliation(s)
- Ines Gruner
- Institute of Microbiology, University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | | | | | | | | | | |
Collapse
|
8
|
Reinbothe C, El Bakkouri M, Buhr F, Muraki N, Nomata J, Kurisu G, Fujita Y, Reinbothe S. Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction. TRENDS IN PLANT SCIENCE 2010; 15:614-24. [PMID: 20801074 DOI: 10.1016/j.tplants.2010.07.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/14/2010] [Accepted: 07/22/2010] [Indexed: 05/21/2023]
Abstract
Photosynthetic organisms require chlorophyll or bacteriochlorophyll for their light trapping and energy transduction activities. The biosynthetic pathways of chlorophyll and bacteriochlorophyll are similar in most of their early steps, except for the reduction of protochlorophyllide (Pchlide) to chlorophyllide. Whereas angiosperms make use of a light-dependent enzyme, cyanobacteria, algae, bryophytes, pteridophytes and gymnosperms contain an additional, light-independent enzyme dubbed dark-operative Pchlide oxidoreductase (DPOR). Anoxygenic photosynthetic bacteria such as Rhodobacter capsulatus and Rhodobacter sphaeroides rely solely on DPOR. Recent atomic resolution of reductase and catalytic components of DPOR from R. sphaeroides and R. capsulatus, respectively, have revealed their similarity to nitrogenase components. In this review, we discuss the two fundamentally different mechanisms of Pchlide reduction in photosynthetic organisms.
Collapse
Affiliation(s)
- Christiane Reinbothe
- Lehrstuhl für Pflanzenphysiologie, Universität Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Lee M, Gräwert T, Quitterer F, Rohdich F, Eppinger J, Eisenreich W, Bacher A, Groll M. Biosynthesis of isoprenoids: crystal structure of the [4Fe-4S] cluster protein IspG. J Mol Biol 2010; 404:600-10. [PMID: 20932974 DOI: 10.1016/j.jmb.2010.09.050] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 11/24/2022]
Abstract
IspG protein serves as the penultimate enzyme of the recently discovered non-mevalonate pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2C-methyl-D-erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 Å. Each subunit of the c(2) symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe-4S] cluster. Homodimer formation involves an extended contact area (about 1100 Å(2)) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 Å(2)). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron-sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the non-mevalonate pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs.
Collapse
Affiliation(s)
- Matthias Lee
- Lehrstuhl für Biochemie, Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010. [PMID: 20885930 PMCID: PMC2946596 DOI: 10.1155/2010/842639] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/26/2010] [Indexed: 11/18/2022]
Abstract
The general importance of the Fe-S cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the Fe-S cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. In the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many Fe-S enzymes are produced to participate in the central metabolic and energetic pathways. De novo formation of intracellular Fe-S clusters does not occur spontaneously but most likely requires the operation of a SufBCD complex of the SUF machinery, which is the only Fe-S cluster biosynthesis system conserved in these archaea. In this paper, a brief introduction to the buildup and maintenance of the intracellular Fe-S world in aerobic and hyperthermoacidophilic crenarchaeotes, mainly Sulfolobus, is given in the biochemical, genetic, and evolutionary context.
Collapse
|
11
|
Muraki N, Nomata J, Ebata K, Mizoguchi T, Shiba T, Tamiaki H, Kurisu G, Fujita Y. X-ray crystal structure of the light-independent protochlorophyllide reductase. Nature 2010; 465:110-4. [PMID: 20400946 DOI: 10.1038/nature08950] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 05/06/2010] [Accepted: 02/22/2010] [Indexed: 11/09/2022]
Abstract
Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.
Collapse
Affiliation(s)
- Norifumi Muraki
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Pieck JC, Hennecke U, Pierik AJ, Friedel MG, Carell T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J Biol Chem 2006; 281:36317-26. [PMID: 16968710 DOI: 10.1074/jbc.m607053200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Geobacillus stearothermophilus splG gene encodes a thermophilic spore photoproduct lyase (SplG) that belongs to the family of radical S-adenosylmethionine (AdoMet) enzymes. The aerobically purified apo-SplG forms a homodimer, which contains one [4Fe-4S] cluster per monomer unit after reconstitution to the holoform. Formation of the [4Fe-4S] cluster was proven by quantification of the amount of iron and sulfur per homodimer and by UV and EPR spectroscopy. The UV spectrum features a characteristic absorbance at 420 nm typical for [4Fe-4S] clusters, and the EPR data were found to be identical to those of other proteins containing an [4Fe-4S]+ center. Probing of the activity of the holo-SplG with oligonucleotides containing one spore photoproduct lesion at a defined site proved that the enzyme is able to turn over substrate. In addition to repair, we observed cleavage of AdoMet to generate 5'-deoxyadenosine. In the presence of aza-AdoMet the SplG is completely inhibited, which provides direct support for the repair mechanism.
Collapse
Affiliation(s)
- J Carsten Pieck
- Department of Chemistry and Biochemistry, Ludwig Maximilians University Munich, D-81377 Munich, Germany
| | | | | | | | | |
Collapse
|
13
|
Wang J, Xue Y, Feng X, Li X, Wang H, Li W, Zhao C, Cheng X, Ma Y, Zhou P, Yin J, Bhatnagar A, Wang R, Liu S. An analysis of the proteomic profile forThermoanaerobacter tengcongensisunder optimal culture conditions. Proteomics 2003; 4:136-50. [PMID: 14730678 DOI: 10.1002/pmic.200300504] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genome of Thermoanaerobacter tengcongensis is estimated to encode 2588 theoretical proteins. In this study, we have vitalized approximately 46% of the theoretical proteome experimentally using a proteomic strategy that combines three different methods, shotgun digestion plus high-performance liquid chromatography (HPLC) with ion-trap tandem mass spectrometry (shotgun-liquid chromatography (LC)/MS), one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) plus HPLC with ion-trap tandem mass spectrometry (one-dimensional electrophoresis (1DE)-LC/MS), and two-dimensional gel electrophoresis plus matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (2DE-MALDI-TOF-MS). Of the 1200 proteins identified, as few as 76 proteins were globally found by all three approaches, and notably, most of these proteins were in the soluble fraction. However, there were a number of unique proteins detected by one method only, suggesting that our strategy provides a means toward obtaining a comprehensive view of protein expression profile. Proteins from the major metabolic pathways are strongly represented on the map, and a number of these enzymes were identified by more than one proteomic method. Based upon the proteins identified in the present study, we are able to broaden the understanding of how T. tengcongensis survives under high temperature environment, whereas several of its properties can not be fully explained by genome data.
Collapse
Affiliation(s)
- Jingqiang Wang
- Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|