Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

Khan, Sharique; Ansari, Ahmadullah; Brachi, Monica; Das, Debarati; El Housseini, Wassim; Minteer, Shelley; Miller, Anne-Frances

doi:10.1016/j.jbc.2024.107122

Title: Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

Journal Article · 28 February 2024 · Journal of Biological Chemistry

DOI: https://doi.org/10.1016/j.jbc.2024.107122 · OSTI ID:2315713

^[1]; Ansari, Ahmadullah ^[2]; Brachi, Monica ^[3]; Das, Debarati ^[1]; El Housseini, Wassim ^[3]; Minteer, Shelley ^[4];

^[1]

University of Kentucky, Lexington, KY (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
University of Utah, Salt Lake City, UT (United States)
University of Utah, Salt Lake City, UT (United States); Missouri University of Science and Technology, Rolla, MO (United States)

The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial en- zymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld’s ability to work with diverse partners, we solved its crystal structure. We observed the canonical fla- vodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize part- ner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein– protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3-¹⁹F-Tyr in place of Tyr has only a modest effect on Rp9Fld’s redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the ¹⁹F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We pro- pose that the loops surrounding the flavin adopt altered con- formations upon binding to partners and may even participate actively in electron transfer.

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Research Organization:: Univ. of Kentucky, Lexington, KY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); National Science Foundation (NSF); USDOE

Grant/Contract Number:: SC0021283; CHE-CMI 2154206

OSTI ID:: 2315713

Alternate ID(s):: OSTI ID: 2477977

Journal Information:: Journal of Biological Chemistry, Vol. 300, Issue 4; Related Information: Supporting information contains 2 tables and 8 figures plus cited references.; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (90)

�ber das neue Oxydationsferment Warburg, Otto; Christian, Walter Die Naturwissenschaften, Vol. 20, Issue 51 https://doi.org/10.1007/BF01504728	journal	December 1932
Potentiometric Study of the Flavins Michaelis, Leonor; Schubert, Maxwell P.; Smythe, C. V. Journal of Biological Chemistry, Vol. 116, Issue 2 https://doi.org/10.1016/S0021-9258(18)74634-6	journal	December 1936
Flavodoxin: A flavoprotein with ferredoxin activity from Clostridium pasteurianum Knight, E.; D'Eustachio, A. J.; Hardy, R. W. F. Biochimica et Biophysica Acta (BBA) - Enzymology and Biological Oxidation, Vol. 113, Issue 3 https://doi.org/10.1016/S0926-6593(66)80025-5	journal	January 1966
Isolation and Characteristics of Flavodoxin from Nitrogen-fixing Clostridium pasteurianum Knight, E.; Hardy, R. W. F. Journal of Biological Chemistry, Vol. 241, Issue 12 https://doi.org/10.1016/S0021-9258(18)96528-2	journal	June 1966
NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductase Cotruvo, J. A.; Stubbe, J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 38 https://doi.org/10.1073/pnas.0807348105	journal	September 2008
The long goodbye: the rise and fall of flavodoxin during plant evolution Pierella Karlusich, J. J.; Lodeyro, A. F.; Carrillo, N. Journal of Experimental Botany, Vol. 65, Issue 18 https://doi.org/10.1093/jxb/eru273	journal	July 2014
The path of electron transfer to nitrogenase in a phototrophic alpha‐proteobacterium Fixen, Kathryn R.; Pal Chowdhury, Nilanjan; Martinez‐Perez, Marta Environmental Microbiology, Vol. 20, Issue 7 https://doi.org/10.1111/1462-2920.14262	journal	July 2018
Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers Campbell, Ian J.; Bennett, George N.; Silberg, Jonathan J. Frontiers in Energy Research, Vol. 7 https://doi.org/10.3389/fenrg.2019.00079	journal	August 2019
Enhanced plant tolerance to iron starvation by functional substitution of chloroplast ferredoxin with a bacterial flavodoxin Tognetti, Vanesa B.; Zurbriggen, Matias D.; Morandi, Eligio N. Proceedings of the National Academy of Sciences, Vol. 104, Issue 27 https://doi.org/10.1073/pnas.0704553104	journal	July 2007
Possible role of a short extra loop of the long-chain flavodoxin from Azotobacter chroococcum in electron transfer to nitrogenase: Complete 1H, 15N and 13C backbone assignments and secondary solution structure of the flavodoxin Peelen, Sjaak; Wijmenga, SybrenS.; Erbel, PaulJ. A. Journal of Biomolecular NMR, Vol. 7, Issue 4 https://doi.org/10.1007/BF00200433	journal	June 1996
The importance of flavodoxin for environmental stress tolerance in photosynthetic microorganisms and transgenic plants. Mechanism, evolution and biotechnological potential Lodeyro, Anabella F.; Ceccoli, Romina D.; Pierella Karlusich, Juan J. FEBS Letters, Vol. 586, Issue 18 https://doi.org/10.1016/j.febslet.2012.07.026	journal	July 2012
Flavodoxin Is Required for the Activation of the Anaerobic Ribonucleotide Reductase Bianchi, V.; Eliasson, R.; Fontecave, M. Biochemical and Biophysical Research Communications, Vol. 197, Issue 2 https://doi.org/10.1006/bbrc.1993.2548	journal	December 1993
WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases Carey, Jannette; Brynda, Jiri; Wolfová, Julie Protein Science, Vol. 16, Issue 10 https://doi.org/10.1110/ps.073018907	journal	October 2007
Characterisation of flavodoxin NADP⁺ oxidoreductase and flavodoxin; key components of electron transfer in Escherichia coli McIver, Lisa; Leadbeater, Claire; Campopiano, Dominic J. European Journal of Biochemistry, Vol. 257, Issue 3 https://doi.org/10.1046/j.1432-1327.1998.2570577.x	journal	November 1998
Solution Structure of the Sulfite Reductase Flavodoxin-like Domain from Escherichia coli ^† ^, ^‡ Sibille, Nathalie; Blackledge, Martin; Brutscher, Bernhard Biochemistry, Vol. 44, Issue 25 https://doi.org/10.1021/bi050437p	journal	June 2005
Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif)-Flavodoxins Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor International Journal of Molecular Sciences, Vol. 14, Issue 1 https://doi.org/10.3390/ijms14011152	journal	January 2013
The nudeoticle sequence of thenifJgene ofKlebsiella pneumoniae Cannon, Maura; Cannon, Frank; Buchanan-Wollaston, Vicky Nucleic Acids Research, Vol. 16, Issue 23 https://doi.org/10.1093/nar/16.23.11379	journal	January 1988
Electron transport to nitrogenase. Purification and characterization of pyruvate:flavodoxin oxidoreductase. The nifJ gene product. Shah, V. K.; Stacey, G.; Brill, W. J. Journal of Biological Chemistry, Vol. 258, Issue 19 https://doi.org/10.1016/S0021-9258(17)44340-7	journal	October 1983
Bacterial Flavodoxins Support Nitric Oxide Production by Bacillus subtilis Nitric-oxide Synthase Wang, Zhi-Qiang; Lawson, Rachel J.; Buddha, Madhavan R. Journal of Biological Chemistry, Vol. 282, Issue 4 https://doi.org/10.1074/jbc.M608206200	journal	January 2007
Biotin Synthase from Escherichiacoli, an Investigation of the Low Molecular Weight and Protein Components Required for Activity inVitro Birch, Olwen M.; Fuhrmann, Martin; Shaw, Nicholas M. Journal of Biological Chemistry, Vol. 270, Issue 32 https://doi.org/10.1074/jbc.270.32.19158	journal	August 1995
Flavodoxin is Required for Conversion of Dethiobiotin to Biotin in Escherichia coli Ifuku, Ohji; Koga, Nobuyoshi; Haze, Shin-ichiro European Journal of Biochemistry, Vol. 224, Issue 1 https://doi.org/10.1111/j.1432-1033.1994.tb20009.x	journal	August 1994
Mapping the interactions between flavodoxin and its physiological partners flavodoxin reductase and cobalamin-dependent methionine synthase Hall, D. A.; Vander Kooi, C. W.; Stasik, C. N. Proceedings of the National Academy of Sciences, Vol. 98, Issue 17 https://doi.org/10.1073/pnas.171168898	journal	August 2001
Activation of Methionine Synthetase by a Reduced Triphosphopyridine Nucleotide-dependent Flavoprotein System Fujii, Katsuhiko; Huennekens, F. M. Journal of Biological Chemistry, Vol. 249, Issue 21 https://doi.org/10.1016/S0021-9258(19)42122-4	journal	November 1974
The Bidirectional NiFe-hydrogenase in Synechocystis sp. PCC 6803 Is Reduced by Flavodoxin and Ferredoxin and Is Essential under Mixotrophic, Nitrate-limiting Conditions Gutekunst, Kirstin; Chen, Xi; Schreiber, Karoline Journal of Biological Chemistry, Vol. 289, Issue 4 https://doi.org/10.1074/jbc.M113.526376	journal	December 2013
Characterization of an Ancestral Type of Pyruvate Ferredoxin Oxidoreductase from the Hyperthermophilic Bacterium, Thermotoga maritima Blamey, Jenny M.; Adams, Michael W. W. Biochemistry, Vol. 33, Issue 4 https://doi.org/10.1021/bi00170a019	journal	February 1994
Routes of Flavodoxin and Ferredoxin Reduction in Escherichia coli: CoA-Acylating Pyruvate: Flavodoxin and NADPH: Flavodoxin Oxidoreductases Participating in the Activation of Pyruvate Formate-Lyase Blaschkowski, Hans P.; Knappe, Joachim; Ludwig-Festl, Monika European Journal of Biochemistry, Vol. 123, Issue 3 https://doi.org/10.1111/j.1432-1033.1982.tb06569.x	journal	April 1982
Helicobacter pylori porCDAB and oorDABCGenes Encode Distinct Pyruvate:Flavodoxin and 2-Oxoglutarate:Acceptor Oxidoreductases Which Mediate Electron Transport to NADP Hughes, Nicky J.; Clayton, Chris L.; Chalk, Peter A. Journal of Bacteriology, Vol. 180, Issue 5 https://doi.org/10.1128/JB.180.5.1119-1128.1998	journal	March 1998
Cytochrome P450cin (CYP176A), Isolation, Expression, and Characterization Hawkes, David B.; Adams, Gregory W.; Burlingame, Alma L. Journal of Biological Chemistry, Vol. 277, Issue 31 https://doi.org/10.1074/jbc.M203382200	journal	August 2002
Chemical and Biological Reduction of the Radical SAM Enzyme CPH ₄ Synthase Bruender, Nathan A.; Young, Anthony P.; Bandarian, Vahe Biochemistry, Vol. 54, Issue 18 https://doi.org/10.1021/acs.biochem.5b00210	journal	April 2015
Surface Charges and Regulation of FMN to Heme Electron Transfer in Nitric-oxide Synthase Tejero, Jesús; Hannibal, Luciana; Mustovich, Anthony Journal of Biological Chemistry, Vol. 285, Issue 35 https://doi.org/10.1074/jbc.M110.138842	journal	August 2010
Roles of negatively charged surface residues of putidaredoxin in interactions with redox partners in P450cam monooxygenase system Aoki, Masaaki; Ishimori, Koichiro; Morishima, Isao Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1386, Issue 1 https://doi.org/10.1016/S0167-4838(98)00094-6	journal	July 1998
Electron acceptor specificity of ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli Wan, Jason T.; Jarrett, Joseph T. Archives of Biochemistry and Biophysics, Vol. 406, Issue 1 https://doi.org/10.1016/S0003-9861(02)00421-6	journal	October 2002
Isolation of Phytoflavin, A Flavoprotein with Chloroplast Ferredoxin Activity Smillie, Robert M. Plant Physiology, Vol. 40, Issue 6 https://doi.org/10.1104/pp.40.6.1124	journal	November 1965
The Long and Short Flavodoxins: I. THE ROLE OF THE DIFFERENTIATING LOOP IN APOFLAVODOXIN STRUCTURE AND FMN BINDING López-Llano, Jon; Maldonado, Susana; Bueno, Marta Journal of Biological Chemistry, Vol. 279, Issue 45 https://doi.org/10.1074/jbc.M405792200	journal	August 2004
Structural basis for energy and electron transfer of the photosystem I–IsiA–flavodoxin supercomplex Cao, Peng; Cao, Duanfang; Si, Long Nature Plants, Vol. 6, Issue 2 https://doi.org/10.1038/s41477-020-0593-7	journal	February 2020
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris Pechter, Kieran B.; Gallagher, Larry; Pyles, Harley Journal of Bacteriology, Vol. 198, Issue 5 https://doi.org/10.1128/JB.00771-15	journal	December 2015
Molecular view of an electron transfer process essential for iron–sulfur protein biogenesis Banci, Lucia; Bertini, Ivano; Calderone, Vito Proceedings of the National Academy of Sciences, Vol. 110, Issue 18 https://doi.org/10.1073/pnas.1302378110	journal	April 2013
Electrochemical and structural characterization of Azotobacter vinelandii flavodoxin II: Segal et al. Segal, Helen M.; Spatzal, Thomas; Hill, Michael G. Protein Science, Vol. 26, Issue 10 https://doi.org/10.1002/pro.3236	journal	August 2017
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
X-ray Crystal Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase ^† ^, ^‡ Silaghi-Dumitrescu, Radu; Kurtz,, Donald M.; Ljungdahl, Lars G. Biochemistry, Vol. 44, Issue 17 https://doi.org/10.1021/bi0473049	journal	May 2005
Enzyme entrapment, biocatalyst immobilization without covalent attachment Imam, Hasan T.; Marr, Patricia C.; Marr, Andrew C. Green Chemistry, Vol. 23, Issue 14 https://doi.org/10.1039/D1GC01852C	journal	January 2021
Anthracene-modified pyrenes immobilized on carbon nanotubes for direct electroreduction of O2 by laccase Giroud, Fabien; Minteer, Shelley D. Electrochemistry Communications, Vol. 34 https://doi.org/10.1016/j.elecom.2013.06.006	journal	September 2013
Comparisons of wild-type and mutant flavodoxins from Anacystis nidulans . Structural determinants of the redox potentials 1 1Edited by R. Huber Hoover, David M.; Drennan, Catherine L.; Metzger, Anita L. Journal of Molecular Biology, Vol. 294, Issue 3 https://doi.org/10.1006/jmbi.1999.3152	journal	December 1999
Differential Stabilization of the Three FMN Redox Forms by Tyrosine 94 and Tryptophan 57 in Flavodoxin from Anabaena and Its Influence on the Redox Potentials ^† Lostao, Anabel; Gómez-Moreno, Carlos; Mayhew, Stephen G. Biochemistry, Vol. 36, Issue 47 https://doi.org/10.1021/bi971384h	journal	November 1997
Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis ^† Seyedsayamdost, Mohammad R.; Reece, Steven Y.; Nocera, Daniel G. Journal of the American Chemical Society, Vol. 128, Issue 5 https://doi.org/10.1021/ja055926r	journal	February 2006
Occurrence of protein structure elements in conserved sequence regions Sitbon, Einat; Pietrokovski, Shmuel BMC Structural Biology, Vol. 7, Issue 1, p. 3 https://doi.org/10.1186/1472-6807-7-3	journal	January 2007
Proteome-pI: proteome isoelectric point database Kozlowski, Lukasz P. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw978	journal	October 2016
Analysis of Domain-Swapped Oligomers Reveals Local Sequence Preferences and Structural Imprints at the Linker Regions and Swapped Interfaces Shingate, Prashant; Sowdhamini, R. PLoS ONE, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pone.0039305	journal	July 2012
Oxidation-reduction potentials of ferredoxin-NADP+ reductase and flavodoxin from Anabaena PCC 7119 and their electrostatic and covalent complexes Pueyo, Jose J.; Gomez-Moreno, Carlos; Mayhew, Stephen G. European Journal of Biochemistry, Vol. 202, Issue 3 https://doi.org/10.1111/j.1432-1033.1991.tb16471.x	journal	December 1991
A theoretical multiscale treatment of protein–protein electron transfer: The ferredoxin/ferredoxin-NADP+ reductase and flavodoxin/ferredoxin-NADP+ reductase systems Saen-oon, Suwipa; Cabeza de Vaca, Israel; Masone, Diego Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1847, Issue 12 https://doi.org/10.1016/j.bbabio.2015.09.002	journal	December 2015
Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP⁺ reductase Kurisu, Genji; Kusunoki, Masami; Katoh, Etsuko Nature Structural Biology, Vol. 8, Issue 2, p. 117-121 https://doi.org/10.1038/84097	journal	February 2001
Dynamics in transient complexes of redox proteins Ubbink, Marcellus Biochemical Society Transactions, Vol. 40, Issue 2 https://doi.org/10.1042/BST20110698	journal	March 2012
Control of Oxidation−Reduction Potentials in Flavodoxin from Clostridium beijerinckii : The Role of Conformation Changes ^† ^, ^‡ Ludwig, Martha L.; Pattridge, Katherine A.; Metzger, Anita L. Biochemistry, Vol. 36, Issue 6 https://doi.org/10.1021/bi962180o	journal	February 1997
A dimer-monomer transition captured by the crystal structures of cyanobacterial apo flavodoxin Liu, Shuwen; Chen, Yuanyuan; Du, Tianming Biochemical and Biophysical Research Communications, Vol. 639 https://doi.org/10.1016/j.bbrc.2022.11.089	journal	January 2023
Backbone dynamics of oxidized and reduced D. vulgaris flavodoxin in solution Hrovat, Andrea; Blümel, Markus; Löhr, Frank Journal of Biomolecular NMR, Vol. 10, Issue 1, p. 53-62 https://doi.org/10.1023/A:1018380509735	journal	July 1997
X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin Mutoh, Risa; Muraki, Norifumi; Shinmura, Kanako Biochemistry, Vol. 54, Issue 39 https://doi.org/10.1021/acs.biochem.5b00601	journal	September 2015
Flavodoxin cofactor binding induces structural changes that are required for protein–protein interactions with NADP+ oxidoreductase and pyruvate formate-lyase activating enzyme Crain, Adam V.; Broderick, Joan B. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 12 https://doi.org/10.1016/j.bbapap.2013.08.014	journal	December 2013
NADPH-cytochrome P-450 oxidoreductase: flavin mononucleotide and flavin adenine dinucleotide domains evolved from different flavoproteins Porter, Todd D.; Kasper, Charles B. Biochemistry, Vol. 25, Issue 7 https://doi.org/10.1021/bi00355a036	journal	April 1986
The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 å resolution Ingelman, Margareta; Bianchi, Vera; Eklund, Hans Journal of Molecular Biology, Vol. 268, Issue 1 https://doi.org/10.1006/jmbi.1997.0957	journal	April 1997
Structural and Kinetic Studies of Asp632 Mutants and Fully Reduced NADPH-Cytochrome P450 Oxidoreductase Define the Role of Asp632 Loop Dynamics in the Control of NADPH Binding and Hydride Transfer Xia, Chuanwu; Rwere, Freeborn; Im, Sangchoul Biochemistry, Vol. 57, Issue 6 https://doi.org/10.1021/acs.biochem.7b01102	journal	January 2018
Confrontation of AlphaFold models with experimental structures enlightens conformational dynamics supporting CYP102A1 functions Urban, Philippe; Pompon, Denis Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-20390-6	journal	September 2022
The Domain Architecture of Cytochrome P450BM-3 Govindaraj, Shanthi; Poulos, Thomas L. Journal of Biological Chemistry, Vol. 272, Issue 12 https://doi.org/10.1074/jbc.272.12.7915	journal	March 1997
The dimeric form of flavocytochrome P450 BM3 is catalytically functional as a fatty acid hydroxylase Neeli, Rajasekhar; Girvan, Hazel M.; Lawrence, Andrew FEBS Letters, Vol. 579, Issue 25 https://doi.org/10.1016/j.febslet.2005.09.023	journal	September 2005
Heterocyst-specific flavodiiron protein Flv3B enables oxic diazotrophic growth of the filamentous cyanobacterium Anabaena sp. PCC 7120 Ermakova, M.; Battchikova, N.; Richaud, P. Proceedings of the National Academy of Sciences, Vol. 111, Issue 30 https://doi.org/10.1073/pnas.1407327111	journal	July 2014
A Flavodiiron Protein and High Molecular Weight Rubredoxin from Moorella thermoacetica with Nitric Oxide Reductase Activity ^† Silaghi-Dumitrescu, Radu; Coulter, Eric D.; Das, Amaresh Biochemistry, Vol. 42, Issue 10 https://doi.org/10.1021/bi027253k	journal	March 2003
Electron hopping through proteins Warren, Jeffrey J.; Ener, Maraia E.; Vlček, Antonín Coordination Chemistry Reviews, Vol. 256, Issue 21-22 https://doi.org/10.1016/j.ccr.2012.03.032	journal	November 2012
Quantitation of proteins using a dye–metal-based colorimetric protein assay Antharavally, Babu S.; Mallia, Krishna A.; Rangaraj, Priya Analytical Biochemistry, Vol. 385, Issue 2 https://doi.org/10.1016/j.ab.2008.11.024	journal	February 2009
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Automated evaluation of quaternary structures from protein crystals Bliven, Spencer; Lafita, Aleix; Parker, Althea PLOS Computational Biology, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pcbi.1006104	journal	April 2018
The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways Zallot, Rémi; Oberg, Nils; Gerlt, John A. Biochemistry, Vol. 58, Issue 41 https://doi.org/10.1021/acs.biochem.9b00735	journal	September 2019
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools Oberg, Nils; Zallot, Rémi; Gerlt, John A. Journal of Molecular Biology, Vol. 435, Issue 14 https://doi.org/10.1016/j.jmb.2023.168018	journal	July 2023
Tertiary structure of two‐electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two‐dimensional ¹H‐NMR and restrained molecular dynamics van MIERLO, Carlo P. M.; Lijnzaad, Philip; Vervoort, Jacques European Journal of Biochemistry, Vol. 194, Issue 1 https://doi.org/10.1111/j.1432-1033.1990.tb19444.x	journal	November 1990
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion Thomsen, Martin Christen Frølund; Nielsen, Morten Nucleic Acids Research, Vol. 40, Issue W1 https://doi.org/10.1093/nar/gks469	journal	May 2012
Tools for integrated sequence-structure analysis with UCSF Chimera Meng, Elaine C.; Pettersen, Eric F.; Couch, Gregory S. BMC Bioinformatics, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2105-7-339	journal	July 2006
Structure of a cytochrome P450-redox partner electron-transfer complex Sevrioukova, I. F.; Li, H.; Zhang, H. Proceedings of the National Academy of Sciences, Vol. 96, Issue 5 https://doi.org/10.1073/pnas.96.5.1863	journal	March 1999
A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii : Structural determinants of redox potential Alagaratnam, Sharmini; van Pouderoyen, Gertie; Pijning, Tjaard Protein Science, Vol. 14, Issue 9 https://doi.org/10.1110/ps.051582605	journal	September 2005
Redox Properties of Wild-Type, Cys69Ala, and Cys69Ser Azotobacter Vinelandii Flavodoxin II as Measured by Cyclic Voltammetry and EPR Spectroscopy Steensma, Elles; Heering, Hendrik A.; Hagen, Wilfred R. European Journal of Biochemistry, Vol. 235, Issue 1-2 https://doi.org/10.1111/j.1432-1033.1996.00167.x	journal	January 1996
SWISS-MODEL: homology modelling of protein structures and complexes Waterhouse, Andrew; Bertoni, Martino; Bienert, Stefan Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky427	journal	May 2018
Structure and function of an unusual flavodoxin from the domain Archaea Prakash, Divya; Iyer, Prashanti R.; Suharti, Suharti Proceedings of the National Academy of Sciences, Vol. 116, Issue 51 https://doi.org/10.1073/pnas.1908578116	journal	December 2019
Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner Hsieh, Yin-Cheng; Chia, Tze; Fun, Hoong-Kun International Journal of Molecular Sciences, Vol. 14, Issue 1 https://doi.org/10.3390/ijms14011667	journal	January 2013
The effects of pH and semiquinone formation on the oxidation-reduction potentials of flavin mononucleotide. A reappraisal Mayhew, Stephen G. European Journal of Biochemistry, Vol. 265, Issue 2 https://doi.org/10.1046/j.1432-1327.1999.00767.x	journal	October 1999
Diversity and complexity of flavodiiron NO/O2 reductases Folgosa, Filipe; Martins, Maria C.; Teixeira, Miguel FEMS Microbiology Letters, Vol. 365, Issue 3 https://doi.org/10.1093/femsle/fnx267	journal	December 2017
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Three-dimensional structure of NADPH-cytochrome P450 reductase: Prototype for FMN- and FAD-containing enzymes Wang, M.; Roberts, D. L.; Paschke, R. Proceedings of the National Academy of Sciences, Vol. 94, Issue 16 https://doi.org/10.1073/pnas.94.16.8411	journal	August 1997

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59 BASIC BIOLOGICAL SCIENCES
36 MATERIALS SCIENCE
60 APPLIED LIFE SCIENCES
electron carrier
flavodoxin
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partner binding
X-ray crystal structure
dynamics
dynamic loops
electron transfer
19F NMR
surface loops

Title: Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

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