Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an α-70Ile MoFe protein variant

Sarma, Ranjana; Barney, Brett M.; Keable, S.M.; Dean, Dennis R.; Seefeldt, Lance C.; Peters, John W.

doi:10.1016/j.jinorgbio.2009.11.009

Cited by 70 publications

(68 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the current study, we limited the calculations to binding at the most commonly proposed sites, the Fe2 and Fe6 ions on the face adjacent to the α -V70 residue. [13c, 22] , see Figure 4. The atom and residue numbering here are as in the crystal structure.…”

Section: Resultsmentioning

confidence: 99%

IR‐Monitored Photolysis of CO‐Inhibited Nitrogenase: A Major EPR‐Silent Species with Coupled Terminal CO Ligands

Yan

Pelmenschikov

Dapper

et al. 2012

Chemistry A European J

View full text Add to dashboard Cite

We have used Fourier transform infrared spectroscopy (FT-IR) to observe the photolysis and recombination of a novel EPR-silent CO-inhibited form of α-H195Q nitrogenase from Azotobacter vinelandii. Photolysis at 4 K yields a strong negative IR difference band at 1938 cm−1, along with a weaker negative feature at 1911 cm−1. These bands and the associated chemical species have both been assigned the label ‘Hi-3’. A positive band at 1921 cm−1 is assigned to the ‘Lo-3’ photoproduct. By using an isotopic mixture of 12C16O and 13C18O, we show that the Hi-3 bands arise from coupling of two similar CO oscillators with one uncoupled frequency at ~1917 cm−1. Although in previous studies Lo-3 was not observed to recombine, by extending the observation range to 200–240 K we found that recombination to Hi-3 does indeed occur, with an activation energy of ~6.5 kJ mol−1. The frequencies of the Hi-3 bands suggest terminal CO ligation. We tested this hypothesis with DFT calculations on models with terminal CO ligands on Fe2 and Fe6 of the FeMo-cofactor. An S = 0 model with both CO ligands in exo positions predicts symmetric and asymmetric stretches at 1938 and 1909 cm−1 respectively, with relative band intensities of ~3.5:1, in good agreement with experiment. From the observed IR intensities, we find that Hi-3 is present at a concentration about equal to that of the EPR-active Hi-1 species. The relevance of Hi-3 to the nitrogenase catalytic mechanism and its recently discovered Fischer-Tropsch chemistry is discussed.

show abstract

Section: Resultsmentioning

confidence: 99%

IR‐Monitored Photolysis of CO‐Inhibited Nitrogenase: A Major EPR‐Silent Species with Coupled Terminal CO Ligands

Yan

Pelmenschikov

Dapper

et al. 2012

Chemistry A European J

View full text Add to dashboard Cite

show abstract

“…For example, the solutions of a number of high-resolution X-ray structures of the nitrogenase component proteins 55−69 have provided insights into the nature of the active site FeMo-cofactor, most recently identifying the presence of an interstitial C atom, 70−77 while structures of the two proteins in the complex 78−81 have identified their binding interface (Figures 1 and 2) and its alterations with the state of the bound nucleotide. 67 Likewise, great strides have been made in understanding the biosynthesis and insertion of the metal clusters of nitrogenase to form the mature proteins, 21,82−89 and the properties of the V-type nitrogenase.…”

Section: Introductionmentioning

confidence: 99%

Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage

et al. 2014

Self Cite

View full text Add to dashboard Cite

Introduction 4041 2. Background 4043 2.1. Kinetics and Stoichiometry 4043 2.2. Trapping and Characterization of Substrates 4044 3. Intermediates of Nitrogenase Activation 4044 3.1. E 1 −E 3 4044 3.2. E 4 : The "Janus Intermediate" 4044 3.3. Redox Behavior and Hydride Chemistry of E 1 −E 3 : Why Such a Big Catalytic Cluster? 4046 3.4. Why Does Nitrogenase Not React with H 2 / D 2 /T 2 in the Absence of N 2 ? 4047 4. "Dueling" N 2 Reduction Pathways 4047 5. Intermediates of N 2 Reduction: E n , n ≥ 4 4048 5.1. Intermediate I 4048 5.2. Nitrogenase Reaction Pathway: D versus A 4048 5.3. Intermediate H 4049 6. Unification of the Nitrogenase Reaction Pathway with the LT Kinetic Scheme 4050 7. Obligatory Evolution of H 2 in Nitrogen Fixation: Reductive Elimination of H 2 4050 7.1. Hydride Protonation (hp) Mechanism 4051 7.2. Reductive Elimination (re) Mechanism 4051 7.3. Mechanistic Constraints Reveal That Nitrogenase Follows the re Mechanisms 4051 8. Test of the re Mechanism 4052 8.1. Predictions 4053 8.2. Testing the Predictions 4053 9. Completing the Mechanism of Nitrogen Fixation 4054 9.1. Uniqueness of N 2 and Nitrogenase 4055 9.2. Structure of the E 4 (N 2 ) Intermediate: Some Implications 4056 10. Summary of Mechanistic Insights 4056 10.1. Catalytic Intermediates of N 2 Fixation 4056 10.2. re Mechanism 4056 10.3. Turnover under N 2 /D 2 /C 2 H 2 as a Test of the re Mechanism 4057 11. Conclusions 4057 Associated Content 4057 Supporting Information 4057 Author Information 4057 Corresponding Authors 4057 Notes 4058 Biographies 4058 Acknowledgments 4058 References 4058

show abstract

“…24,25,27 Spectroscopic studies further support the idea that the iron-vanadium cofactor (FeVco) contains an interstitial carbide like the FeMoco. 28,29 The shared cluster type in various nitrogenases, and studies on the activity and spectroscopy of variants of the FeMo enzyme that derive from point mutations, 30–33 indicate that the belt iron sites (indicated in red in Fig. 1) are the site of N 2 binding and reduction.…”

Section: Introductionmentioning

confidence: 99%

Insight into the Iron–Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

2016

View full text Add to dashboard Cite

Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small molecule activation. Here, we review recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon and sulfur based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.

show abstract

Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an α-70Ile MoFe protein variant

Cited by 70 publications

References 33 publications

IR‐Monitored Photolysis of CO‐Inhibited Nitrogenase: A Major EPR‐Silent Species with Coupled Terminal CO Ligands

IR‐Monitored Photolysis of CO‐Inhibited Nitrogenase: A Major EPR‐Silent Species with Coupled Terminal CO Ligands

Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage

Insight into the Iron–Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

Contact Info

Product

Resources

About