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Roy RR, Ullmann GM. Virtual Model Compound Approach for Calculating Redox Potentials of [Fe 2S 2]-Cys 4 Centers in Proteins - Structure Quality Matters. J Chem Theory Comput 2023; 19:8930-8941. [PMID: 37974307 DOI: 10.1021/acs.jctc.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The midpoint potential of the [Fe2S2]-Cys4-cluster in proteins is known to vary between -200 and -450 mV. This variation is caused by the different electrostatic environment of the cluster in the respective proteins. Continuum electrostatics can quantify the impact of the protein environment on the redox potential. Thus, if the redox potential of a [Fe2S2]-Cys4-cluster model compound in aqueous solution would be known, then redox potentials in various protein complexes could be calculated. However, [Fe2S2]-Cys4-cluster models are not water-soluble, and thus, their redox potential can not be measured in aqueous solution. To overcome this problem, we introduce a method that we call Virtual Model Compound Approach (VMCA) to extrapolate the model redox potential from known redox potentials of proteins. We carefully selected high-resolution structures for our analysis and divide them into a fit set, for fitting the model redox potential, and an independent test set, to check the validity of the model redox potential. However, from our analysis, we realized that the some structures can not be used as downloaded from the PDB but had to be re-refined in order to calculate reliable redox potentials. Because of the re-refinement, we were able to significantly reduce the standard deviation of our derived model redox potential for the [Fe2S2]-Cys4-cluster from 31 mV to 10 mV. As the model redox potential, we obtained -184 mV. This model redox potential can be used to analyze the redox behavior of [Fe2S2]-Cys4-clusters in larger protein complexes.
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Affiliation(s)
- Rajeev Ranjan Roy
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
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2
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Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms232415913. [PMID: 36555561 PMCID: PMC9782105 DOI: 10.3390/ijms232415913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
"Plant-type" ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds.
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3
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Ohnishi Y, Muraki N, Kiyota D, Okumura H, Baba S, Kawano Y, Kumasaka T, Tanaka H, Kurisu G. X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii. J Biochem 2020; 167:549-555. [PMID: 32282907 DOI: 10.1093/jb/mvaa045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 12/28/2019] [Indexed: 11/13/2022] Open
Abstract
Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported so far, very likely a given number of them was partially reduced by strong X-ray. To understand the precise structural change between reduced and oxidized Fd, it is important to know whether the crystals of oxidized Fd may or may not be reduced during the X-ray experiment. We prepared the thin plate-shaped Fd crystals from Chlamydomonas reinhardtii and monitored its absorption spectra during experiment. Absorption spectra of oxidized Fd crystals were clearly changed to that of reduced form in an X-ray dose-dependent manner. In another independent experiment, the X-ray diffraction images obtained from different parts of one single crystal were sorted and merged to form two datasets with low and high X-ray doses. An Fo-Fo map calculated from the two datasets showed that X-ray reduction causes a small displacement of the iron atoms in the [2Fe-2S] cluster. Both our spectroscopic and crystallographic studies confirm X-ray dose-dependent reduction of Fd, and suggest a structural basis for its initial reduction step especially in the core of the cluster.
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Affiliation(s)
- Yusuke Ohnishi
- Division of Protein Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Norifumi Muraki
- Division of Protein Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daiki Kiyota
- Division of Protein Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideo Okumura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Hideaki Tanaka
- Division of Protein Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Genji Kurisu
- Division of Protein Structural Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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4
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An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148084. [DOI: 10.1016/j.bbabio.2019.148084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 11/23/2022]
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5
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Campbell IJ, Bennett GN, Silberg JJ. Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. FRONTIERS IN ENERGY RESEARCH 2019; 7:10.3389/fenrg.2019.00079. [PMID: 32095484 PMCID: PMC7039249 DOI: 10.3389/fenrg.2019.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (~13), Bacteria (~8), and Eukarya (~3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.
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Affiliation(s)
- Ian J. Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, TX, United States
| | - George N. Bennett
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University Houston, TX, United States
- Correspondence: Jonathan J. Silberg
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6
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Mutoh R, Muraki N, Shinmura K, Kubota-Kawai H, Lee YH, Nowaczyk MM, Rögner M, Hase T, Ikegami T, Kurisu G. X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin. Biochemistry 2015; 54:6052-61. [DOI: 10.1021/acs.biochem.5b00601] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Risa Mutoh
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Norifumi Muraki
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Kanako Shinmura
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Hisako Kubota-Kawai
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Young-Ho Lee
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Marc M. Nowaczyk
- Plant
Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Matthias Rögner
- Plant
Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Toshiharu Hase
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Takahisa Ikegami
- Department
of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Genji Kurisu
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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7
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Tikhonov AN. Induction events and short-term regulation of electron transport in chloroplasts: an overview. PHOTOSYNTHESIS RESEARCH 2015; 125:65-94. [PMID: 25680580 DOI: 10.1007/s11120-015-0094-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/26/2015] [Indexed: 05/03/2023]
Abstract
Regulation of photosynthetic electron transport at different levels of structural and functional organization of photosynthetic apparatus provides efficient performance of oxygenic photosynthesis in plants. This review begins with a brief overview of the chloroplast electron transport chain. Then two noninvasive biophysical methods (measurements of slow induction of chlorophyll a fluorescence and EPR signals of oxidized P700 centers) are exemplified to illustrate the possibility of monitoring induction events in chloroplasts in vivo and in situ. Induction events in chloroplasts are considered and briefly discussed in the context of short-term mechanisms of the following regulatory processes: (i) pH-dependent control of the intersystem electron transport; (ii) the light-induced activation of the Calvin-Benson cycle; (iii) optimization of electron transport due to fitting alternative pathways of electron flow and partitioning light energy between photosystems I and II; and (iv) the light-induced remodeling of photosynthetic apparatus and thylakoid membranes.
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin. PLoS One 2011; 6:e21947. [PMID: 21760931 PMCID: PMC3132287 DOI: 10.1371/journal.pone.0021947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/13/2011] [Indexed: 11/19/2022] Open
Abstract
Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd), a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at 1.46 Å resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short α-helix (67-71) near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes.
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10
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Senda T, Senda M, Kimura S, Ishida T. Redox control of protein conformation in flavoproteins. Antioxid Redox Signal 2009; 11:1741-66. [PMID: 19243237 DOI: 10.1089/ars.2008.2348] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are two flavin prosthetic groups utilized as the redox centers of various proteins. The conformations and chemical properties of these flavins can be affected by their redox states as well as by photoreactions. Thus, proteins containing flavin (flavoproteins) can function not only as redox enzymes, but also as signaling molecules by using the redox- and/or light-dependent changes of the flavin. Redox and light-dependent conformational changes of flavoproteins are critical to many biological signaling systems. In this review, we summarize the molecular mechanisms of the redox-dependent conformational changes of flavoproteins and discuss their relationship to signaling functions. The redox-dependent (or light-excited) changes of flavin and neighboring residues in proteins act as molecular "switches" that "turn on" various conformational changes in proteins, and can be classified into five types. On the basis of the present analysis, we recommend future directions in molecular structural research on flavoproteins and related proteins.
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Affiliation(s)
- Toshiya Senda
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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11
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Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii. Biophys J 2008; 95:3753-66. [PMID: 18621810 DOI: 10.1529/biophysj.107.127548] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer.
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12
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Chang CH, King PW, Ghirardi ML, Kim K. Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii. Biophys J 2007; 93:3034-45. [PMID: 17660315 PMCID: PMC2025642 DOI: 10.1529/biophysj.107.108589] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 07/06/2007] [Indexed: 11/18/2022] Open
Abstract
The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H(2) from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H(2) evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2.
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Nascimento AS, Ferrarezi T, Catalano-Dupuy DL, Ceccarelli EA, Polikarpov I. Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:662-4. [PMID: 16820688 PMCID: PMC2242957 DOI: 10.1107/s1744309106020136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Accepted: 05/29/2006] [Indexed: 11/10/2022]
Abstract
Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 angstroms resolution at a synchrotron source.
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Affiliation(s)
- Alessandro S. Nascimento
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Thiago Ferrarezi
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Daniela L. Catalano-Dupuy
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
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