Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

Kang, Wonchull; Lee, Chi Chung; Jasniewski, Andrew J.; Ribbe, Markus W.; Hu, Yilin

doi:10.1126/science.aaz6748

Title: Structural evidence for a dynamic metallocofactor during N ₂ reduction by Mo-nitrogenase

Journal Article · Thu Jun 18 00:00:00 EDT 2020 · Science

DOI:https://doi.org/10.1126/science.aaz6748· OSTI ID:1803014

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Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.
Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.; Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N₂) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N₂turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

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Research Organization:: Univ. of California, Irvine, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0016510

OSTI ID:: 1803014

Journal Information:: Science, Vol. 368, Issue 6497; ISSN 0036-8075

Publisher:: AAAS

Country of Publication:: United States

Language:: English

References (40)

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
Structural basis of biological nitrogen fixation Rees, Douglas C.; Akif Tezcan, F.; Haynes, Chad A. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 363, Issue 1829 https://doi.org/10.1098/rsta.2004.1539	journal	April 2005
Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage Hoffman, Brian M.; Lukoyanov, Dmitriy; Yang, Zhi-Yong Chemical Reviews, Vol. 114, Issue 8 https://doi.org/10.1021/cr400641x	journal	January 2014
Radical SAM-Dependent Carbon Insertion into the Nitrogenase M-Cluster Wiig, J. A.; Hu, Y.; Lee, C. C. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1224603	journal	September 2012
Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor Spatzal, T.; Aksoyoglu, M.; Zhang, L. Science, Vol. 334, Issue 6058 https://doi.org/10.1126/science.1214025	journal	November 2011
Vanadium Nitrogenase Reduces CO Lee, C. C.; Hu, Y.; Ribbe, M. W. Science, Vol. 329, Issue 5992 https://doi.org/10.1126/science.1191455	journal	August 2010
Extending the Carbon Chain: Hydrocarbon Formation Catalyzed by Vanadium/Molybdenum Nitrogenases Hu, Y.; Lee, C. C.; Ribbe, M. W. Science, Vol. 333, Issue 6043 https://doi.org/10.1126/science.1206883	journal	August 2011
The mechanism of Klebsiella pneumoniae nitrogenase action. Pre-steady-state kinetics of H2 formation Lowe, D. J.; Thorneley, R. N. Biochemical Journal, Vol. 224, Issue 3 https://doi.org/10.1042/bj2240877	journal	December 1984
The mechanism of Klebsiella pneumoniae nitrogenase action. Pre-steady-state kinetics of an enzyme-bound intermediate in N2 reduction and of NH3 formation Thorneley, R. N. F.; Lowe, D. J. Biochemical Journal, Vol. 224, Issue 3 https://doi.org/10.1042/bj2240887	journal	December 1984
Investigation of CO Binding and Release from Mo-Nitrogenase during Catalytic Turnover ^† Cameron, Linda M.; Hales, Brian J. Biochemistry, Vol. 37, Issue 26 https://doi.org/10.1021/bi972667c	journal	June 1998
Speculative synthetic chemistry and the nitrogenase problem Lee, S. C.; Holm, R. H. Proceedings of the National Academy of Sciences, Vol. 100, Issue 7 https://doi.org/10.1073/pnas.0630028100	journal	March 2003
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
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
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
Redox-Dependent Structural Changes in the Nitrogenase P-Cluster ^† ^, ^‡ Peters, John W.; Stowell, Michael H. B.; Soltis, S. Michael Biochemistry, Vol. 36, Issue 6 https://doi.org/10.1021/bi9626665	journal	February 1997
Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer Owens, Cedric P.; Katz, Faith E. H.; Carter, Cole H. Journal of the American Chemical Society, Vol. 138, Issue 32 https://doi.org/10.1021/jacs.6b06783	journal	August 2016
Redox properties and EPR spectroscopy of the P clusters of Azotobacter vinelandii MoFe protein Pierik, Antonio J.; Wassink, Hans; Haaker, Huub European Journal of Biochemistry, Vol. 212, Issue 1 https://doi.org/10.1111/j.1432-1033.1993.tb17632.x	journal	February 1993
Role of the MoFe Protein .alpha.-Subunit Histidine-195 Residue in FeMo-cofactor Binding and Nitrogenase Catalysis Kim, Chul-Hwan; Newton, William E.; Dean, Dennis R. Biochemistry, Vol. 34, Issue 9 https://doi.org/10.1021/bi00009a008	journal	March 1995
Interaction of Acetylene and Cyanide with the Resting State of Nitrogenase α-96-Substituted MoFe Proteins ^† Benton, Paul M. C.; Mayer, Suzanne M.; Shao, Junlong Biochemistry, Vol. 40, Issue 46 https://doi.org/10.1021/bi011571m	journal	November 2001
Unusual Thiolate-Bridged Diiron Clusters Bearing the cis -HN═NH Ligand and Their Reactivities with Terminal Alkynes Chen, Yanhui; Liu, Litao; Peng, Ying Journal of the American Chemical Society, Vol. 133, Issue 5 https://doi.org/10.1021/ja105948r	journal	February 2011
Ammonia formation by a thiolate-bridged diiron amide complex as a nitrogenase mimic Li, Yang; Li, Ying; Wang, Baomin Nature Chemistry, Vol. 5, Issue 4 https://doi.org/10.1038/nchem.1594	journal	March 2013
The FeMoco-deficient MoFe Protein Produced by a nifH Deletion Strain of Azotobacter vinelandii Shows Unusual P-cluster Features Ribbe, Markus W.; Hu, Yilin; Guo, Maolin Journal of Biological Chemistry, Vol. 277, Issue 26 https://doi.org/10.1074/jbc.M202061200	journal	April 2002
Large-scale purification of high activity Azotobacter vinelandii nitrogenase Burgess, Barbara K.; Jacobs, Deloria B.; Stiefel, Edward I. Biochimica et Biophysica Acta (BBA) - Enzymology, Vol. 614, Issue 1 https://doi.org/10.1016/0005-2744(80)90180-1	journal	July 1980
Catalytic Determination of Vanadium in Water. Fishman, M. J.; Skougstad, M. W. Analytical Chemistry, Vol. 36, Issue 8 https://doi.org/10.1021/ac60214a049	journal	July 1964
Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens Chaikuad, Apirat; Knapp, Stefan; von Delft, Frank Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 8 https://doi.org/10.1107/S1399004715007968	journal	July 2015
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
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
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
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
Experimental phasing with SHELXC / D / E : combining chain tracing with density modification Sheldrick, George M. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444909038360	journal	March 2010
ANODE : anomalous and heavy-atom density calculation Thorn, Andrea; Sheldrick, George M. Journal of Applied Crystallography, Vol. 44, Issue 6 https://doi.org/10.1107/S0021889811041768	journal	November 2011
Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement Cao, Lili; Caldararu, Octav; Ryde, Ulf The Journal of Physical Chemistry B, Vol. 121, Issue 35 https://doi.org/10.1021/acs.jpcb.7b02714	journal	August 2017
A Major Structural Change of the Homocitrate Ligand of Probable Importance for the Nitrogenase Mechanism Siegbahn, Per E. M. Inorganic Chemistry, Vol. 57, Issue 3 https://doi.org/10.1021/acs.inorgchem.7b02493	journal	January 2018
Comparative Assessment of the Composition and Charge State of Nitrogenase FeMo-Cofactor Harris, Travis V.; Szilagyi, Robert K. Inorganic Chemistry, Vol. 50, Issue 11 https://doi.org/10.1021/ic102446n	journal	June 2011
ATP Synthase Junge, Wolfgang; Nelson, Nathan Annual Review of Biochemistry, Vol. 84, Issue 1 https://doi.org/10.1146/annurev-biochem-060614-034124	journal	June 2015
Atomic model for the dimeric F _O region of mitochondrial ATP synthase Guo, Hui; Bueler, Stephanie A.; Rubinstein, John L. Science, Vol. 358, Issue 6365 https://doi.org/10.1126/science.aao4815	journal	October 2017
Biosynthesis of the Metalloclusters of Nitrogenases Hu, Yilin; Ribbe, Markus W. Annual Review of Biochemistry, Vol. 85, Issue 1 https://doi.org/10.1146/annurev-biochem-060614-034108	journal	June 2016
Biosynthesis of Nitrogenase Metalloclusters Ribbe, Markus W.; Hu, Yilin; Hodgson, Keith O. Chemical Reviews, Vol. 114, Issue 8 https://doi.org/10.1021/cr400463x	journal	December 2013
The mechanism for nitrogenase including all steps Siegbahn, Per E. M. Physical Chemistry Chemical Physics, Vol. 21, Issue 28 https://doi.org/10.1039/C9CP02073J	journal	January 2019

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