Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S] 2+/1+/0 States of the Nitrogenase Fe-Protein

Wenke, Belinda B.; Spatzal, Thomas; Rees, Douglas C.

doi:10.1002/anie.201813966

Title: Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S] ^2+/1+/0 States of the Nitrogenase Fe-Protein

Journal Article · Mon Mar 18 00:00:00 EDT 2019 · Angewandte Chemie (International Edition)

DOI:https://doi.org/10.1002/anie.201813966· OSTI ID:1623488

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California Institute of Technology (CalTech), Pasadena, CA (United States). Division of Chemistry and Chemical Engineering
California Institute of Technology (CalTech), Pasadena, CA (United States). Howard Hughes Medical Institute; California Institute of Technology (CalTech), Pasadena, CA (United States). Division of Chemistry and Chemical Engineering

The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2 + , 1 + , and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-c resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionitereduced [4Fe:4S]1+ state, our analysis identifies a solvent exposed, delocalized Fe2.5+ pair and a buried Fe2+ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]0 and [4Fe:4S]2+ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe2+ and valence delocalized Fe2.5+ , respectively.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1623488

Journal Information:: Angewandte Chemie (International Edition), Vol. 58, Issue 12; ISSN 1433-7851

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (33)

Mössbauer and EPR Evidence for an All-Ferrous Fe ₄ S ₄ Cluster with S = 4 in the Fe Protein of Nitrogenase Angove, Hayley C.; Yoo, Sun Jae; Burgess, Barbara K. Journal of the American Chemical Society, Vol. 119, Issue 37 https://doi.org/10.1021/ja9712837	journal	September 1997
Insights into Nucleotide Signal Transduction in Nitrogenase: Structure of an Iron Protein with MgADP Bound ^† ^, ^‡ Jang, Se Bok; Seefeldt, Lance C.; Peters, John W. Biochemistry, Vol. 39, Issue 48 https://doi.org/10.1021/bi001705g	journal	December 2000
All-Ferrous Titanium(III) Citrate Reduced Fe Protein of Nitrogenase: An XAS Study of Electronic and Metrical Structure Musgrave, Kristin B.; Angove, Hayley C.; Burgess, Barbara K. Journal of the American Chemical Society, Vol. 120, Issue 21 https://doi.org/10.1021/ja980598z	journal	June 1998
Flavodoxin hydroquinone reduces Azotobacter vinelandii Fe protein to the all-ferrous redox state with a S = 0 spin state Lowery, T. J.; Wilson, P. E.; Zhang, B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 46 https://doi.org/10.1073/pnas.0603223103	journal	November 2006
Iron-Sulfur Clusters: Nature's Modular, Multipurpose Structures Beinert, H. Science, Vol. 277, Issue 5326 https://doi.org/10.1126/science.277.5326.653	journal	August 1997
Mössbauer and Integer-Spin EPR Studies and Spin-Coupling Analysis of the [4Fe-4S] ⁰ Cluster of the Fe Protein from Azotobacter vinelandii Nitrogenase Yoo, Sun Jae; Angove, Hayley C.; Burgess, Barbara K. Journal of the American Chemical Society, Vol. 121, Issue 11 https://doi.org/10.1021/ja9837405	journal	March 1999
The Sixteenth Iron in the Nitrogenase MoFe Protein Zhang, Limei; Kaiser, Jens T.; Meloni, Gabriele Angewandte Chemie, Vol. 125, Issue 40 https://doi.org/10.1002/ange.201303877	journal	August 2013
Electron-Paramagnetic-Resonance Studies on Nitrogenase. Investigation of the Oxidation-Reduction Behaviour of Azoferredoxin and Molybdoferredoxin with Potentiometric and Rapid-Freeze Techniques Zumft, Walter G.; Mortenson, Leonard E.; Palmer, Graham European Journal of Biochemistry, Vol. 46, Issue 3 https://doi.org/10.1111/j.1432-1033.1974.tb03646.x	journal	August 1974
Crystal Structure of the All-Ferrous [4Fe-4S] ⁰ Form of the Nitrogenase Iron Protein from Azotobacter vinelandii ^† ^, ^‡ Strop, Pavel; Takahara, Patricia M.; Chiu, Hsiu-Ju Biochemistry, Vol. 40, Issue 3 https://doi.org/10.1021/bi0016467	journal	January 2001
Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii Georgiadis, M.; Komiya, H.; Chakrabarti, P. Science, Vol. 257, Issue 5077 https://doi.org/10.1126/science.1529353	journal	September 1992
How many metals does it take to fix N2? A mechanistic overview of biological nitrogen fixation Howard, J. B.; Rees, D. C. Proceedings of the National Academy of Sciences, Vol. 103, Issue 46 https://doi.org/10.1073/pnas.0603978103	journal	November 2006
Circular Dichroism and X-ray Spectroscopies of Azotobacter vinelandii Nitrogenase Iron Protein : MgATP AND MgADP INDUCED PROTEIN CONFORMATIONAL CHANGES AFFECTING THE [4Fe-4S] CLUSTER AND CHARACTERIZATION OF A [2Fe-2S] FORM Ryle, Matthew J.; Lanzilotta, William N.; Seefeldt, Lance C. Journal of Biological Chemistry, Vol. 271, Issue 3 https://doi.org/10.1074/jbc.271.3.1551	journal	January 1996
Effect of magnesium adenosine 5'-triphosphate on the accessibility of the iron of clostridial azoferredoxin, a component of nitrogenase Walker, Gustavus A.; Mortenson, Leonard E. Biochemistry, Vol. 13, Issue 11 https://doi.org/10.1021/bi00708a023	journal	May 1974
Orbital interactions, electron delocalization and spin coupling in iron-sulfur clusters Noodleman, L.; Peng, C. Y.; Case, D. A. Coordination Chemistry Reviews, Vol. 144 https://doi.org/10.1016/0010-8545(95)07011-L	journal	October 1995
Multitemperature Resonance-Diffraction and Structural Study of the Mixed-Valence Complex [Fe ₃ O(OOCC(CH ₃ ) ₃ ) ₆ (C ₅ H ₅ N) ₃ ] Wu, Guang; Zhang, Yuegang; Ribaud, Lynn Inorganic Chemistry, Vol. 37, Issue 23 https://doi.org/10.1021/ic980556b	journal	November 1998
Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor Spatzal, Thomas; Perez, Kathryn A.; Howard, James B. eLife, Vol. 4 https://doi.org/10.7554/eLife.11620	journal	December 2015
Electron paramagnetic resonance studies on nitrogenase. II. Interaction of adenosine 5′-triphosphate with azoferredoxin Zumft, Walter G.; Palmer, Graham; Mortenson, Leonard E. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 292, Issue 2 https://doi.org/10.1016/0005-2728(73)90047-9	journal	February 1973
Nitrogenase: the reaction between iron protein and bathophenanthrolinedisulfonate as a probe for interactions with MgATP Ljones, Torbjorn; Burris, R. H. Biochemistry, Vol. 17, Issue 10 https://doi.org/10.1021/bi00603a010	journal	May 1978
A bound reaction intermediate sheds light on the mechanism of nitrogenase Sippel, Daniel; Rohde, Michael; Netzer, Julia Science, Vol. 359, Issue 6383 https://doi.org/10.1126/science.aar2765	journal	March 2018
Ligand binding to the FeMo-cofactor: Structures of CO-bound and reactivated nitrogenase Spatzal, T.; Perez, K. A.; Einsle, O. Science, Vol. 345, Issue 6204 https://doi.org/10.1126/science.1256679	journal	September 2014
Formation of an all ferrous Fe4S4 cluster in the iron protein component of Azotobacter vinelandii nitrogenase Watt, Gerald D.; Reddy, K. R. N. Journal of Inorganic Biochemistry, Vol. 53, Issue 4 https://doi.org/10.1016/0162-0134(94)85115-8	journal	March 1994
Circular dichroism and magnetic circular dichroism of nitrogenase proteins Stephens, P. J.; McKenna, C. E.; Smith, B. E. Proceedings of the National Academy of Sciences, Vol. 76, Issue 6 https://doi.org/10.1073/pnas.76.6.2585	journal	June 1979
Assignment of Individual Metal Redox States in a Metalloprotein by Crystallographic Refinement at Multiple X-ray Wavelengths Einsle, Oliver; Andrade, Susana L. A.; Dobbek, Holger Journal of the American Chemical Society, Vol. 129, Issue 8 https://doi.org/10.1021/ja067562o	journal	February 2007
Energy Transduction in Nitrogenase Seefeldt, Lance C.; Hoffman, Brian M.; Peters, John W. Accounts of Chemical Research, Vol. 51, Issue 9 https://doi.org/10.1021/acs.accounts.8b00112	journal	August 2018
Mechanism of Molybdenum Nitrogenase Burgess, Barbara K.; Lowe, David J. Chemical Reviews, Vol. 96, Issue 7 https://doi.org/10.1021/cr950055x	journal	January 1996
Enhanced Efficiency of ATP Hydrolysis during Nitrogenase Catalysis Utilizing Reductants That Form the All-Ferrous Redox State of the Fe Protein Erickson, J. Alan; Nyborg, Andrew C.; Johnson, Joseph L. Biochemistry, Vol. 38, Issue 43 https://doi.org/10.1021/bi991389+	journal	October 1999
X-ray Absorption and Emission Spectroscopic Studies of [L ₂ Fe ₂ S ₂ ] ⁿ Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters Kowalska, Joanna K.; Hahn, Anselm W.; Albers, Antonia Inorganic Chemistry, Vol. 55, Issue 9 https://doi.org/10.1021/acs.inorgchem.6b00295	journal	April 2016
The structure of vanadium nitrogenase reveals an unusual bridging ligand Sippel, Daniel; Einsle, Oliver Nature Chemical Biology, Vol. 13, Issue 9 https://doi.org/10.1038/nchembio.2428	journal	July 2017
The Sixteenth Iron in the Nitrogenase MoFe Protein Zhang, Limei; Kaiser, Jens T.; Meloni, Gabriele Angewandte Chemie International Edition, Vol. 52, Issue 40 https://doi.org/10.1002/anie.201303877	journal	August 2013
Evidence for a Two-Electron Transfer Using the All-Ferrous Fe Protein during Nitrogenase Catalysis Nyborg, Andrew C.; Johnson, Joseph L.; Gunn, Alexander Journal of Biological Chemistry, Vol. 275, Issue 50 https://doi.org/10.1074/jbc.M007069200	journal	September 2000
An All-ferrous State of the Fe Protein of Nitrogenase: INTERACTION WITH NUCLEOTIDES AND ELECTRON TRANSFER TO THE MoFe PROTEIN Angove, Hayley C.; Yoo, Sun Jae; Münck, Eckard Journal of Biological Chemistry, Vol. 273, Issue 41 https://doi.org/10.1074/jbc.273.41.26330	journal	October 1998
Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement Spatzal, Thomas; Schlesier, Julia; Burger, Eva-Maria Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10902	journal	March 2016
Structural Models of the [Fe ₄ S ₄ ] Clusters of Homologous Nitrogenase Fe Proteins Blank, Michael A.; Lee, Chi Chung; Hu, Yilin Inorganic Chemistry, Vol. 50, Issue 15 https://doi.org/10.1021/ic200636k	journal	August 2011

Cited By (3)

Structural and Mechanistic Insights into CO ₂ Activation by Nitrogenase Iron Protein Rettberg, Lee A.; Stiebritz, Martin T.; Kang, Wonchull Chemistry – A European Journal, Vol. 25, Issue 57 https://doi.org/10.1002/chem.201903387	journal	September 2019
Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computing Miyagawa, Koichi; Shoji, Mitsuo; Isobe, Hiroshi Molecular Physics, Vol. 118, Issue 21-22 https://doi.org/10.1080/00268976.2020.1760388	journal	May 2020
Theory of chemical bonds in metalloenzymes XXIV electronic and spin structures of FeMoco and Fe-S clusters by classical and quantum computing Miyagawa, Koichi; Shoji, Mitsuo; Isobe, Hiroshi Taylor & Francis https://doi.org/10.6084/m9.figshare.12349784	text	January 2020

Figures / Tables (4)

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Chemistry
iron-sulphur cluster
multiple-wavelength anomalous diffraction
nitrogenase
x-ray crystallography

Title: Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S] 2+/1+/0 States of the Nitrogenase Fe-Protein

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