Saturday, April 30, 2011

Vote Nitrogenase!

Figure 1: Nitrogenase. PDB: 1M1N

Nitrogenase, an enzyme produced by bacteria in the root nodules of many legumes, performs the important nitrogen fixation reaction:

N≡N → 2 NH3
(not balanced)

But why does it deserve your vote?

1This transformation is incredible. Consider this: the N=N bond is 945 kJ/mol strong. This makes nitrogen gas incredibly difficult to reduce. But nitrogenase does it. It has also been shown to split other molecules in vitro, such as carbon dioxide and ethene.

2Nitrogenase does it better than Haber-Bosch. If you recall the Haber-Bosch process, you may remember that to perform the same reaction shown above, an iron catalyst, calcium, potassium, and aluminum oxides, temperatures between 300 and 500˚C, and pressures of 15-20 MPa are required. Nitrogenase performs the same reaction under biological temperatures and pressures with 8 electrons, 8 protons and 16 ATP per transformation. Looks like this enzyme has got us beat.

3Sweet cofactors. Fe-S clusters? Right on. Molybdenum-Fe-S clusters? Even better. What exactly does the molybdenum do? Scientists have yet to provide a definitive answer to that question. 

Figure 2: Molybdenum-Iron-Sulfur Cluster in Nitrogenase protein. PDB: 1MIO.

46 bonds to Carbon! To the horror of organic chemists, nitrogenase's ability to split a variety of organic molecules other than nitrogen gas implicates the existence of a six-coordinate atom within the Mo-Fe-S cluster. The reality of this coordination has not been officially confirmed by bioinorganic chemists, but remains an accepted conclusion in many circles[1].
Figure 3: Schematic drawing of six-coordinate center. Speculation suggests that a carbon atom could exist in this coordination, but the majority of published articles assume it to be a nitrogen atom[2].

 Vote Nitrogenase!

[1] For more information, feel free to chat with Professor David Benson of the Calvin College Chemistry and Biochemistry Department.
[2] Einsle, O., Tezcan, F., Andrade, S., Schmid, B., Yoshida, M., Howard, J., Rees, D. Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the Fe-Mo cofactor. Science 297, 1696-1699.

Friday, March 18, 2011

Nitrogenase: Not Just Another "Bosch-up"

Atmospheric nitrogen is extremely stable. Even the traditional Lewis representation of the homodiatomic molecule, :N=N:, gives some indication of the enormous amounts of energy required to break this triple bond. Industrially the degradation of nitrogen was accomplished through the Haber-Bosch process, which employs the use of an iron catalyst along with calcium, potassium, and aluminum oxides, temperatures from between 300-500˚C, and pressures of 15-20 MPa. The Haber-Bosch process was hailed for its use in fertilizer production, as many believe the current human population could not have been sustained without it, but its harsh conditions and its potential use in explosives manufacturing cause some to view this reaction with disdain.
N2 + 3 H2  2 NH3
The biological fixation of nitrogen in to ammonia, however, should not be viewed with distaste as the Haber-Bosch process perhaps warrants. For millions of years bacterial species have fixed the extremely stable atmospheric nitrogen - the results being nothing but beneficial. The process is energetically taxing, but is efficiently accomplished by the work of an enzyme known as Nitrogenase. 

Nitrogenase isolated from Azotobacter vinelandii was shown to be a dimer, with one subunit containing a Fe cofactor and the other containing a Mo-Fe cofactor. The Fe subunit functions to provide a constant electron flow from ATP breakdown in order to fuel the Mo-Fe subunit's scission of the :N=N: bond[1]. These two subunits are shown to covalently cross-link between a glutamine residue on the Fe subunit and a lysine residue on the MoFe subunit during the catalytic mechanism[2]. Other mechanistic studies have isolated a hexa-coordinated ligand within the Fe-Mo complex, which is argued to be a single nitrogen atom[3]. The implication is that the enzymatic stabilization of the lone nitrogen atom greatly contributes to the efficacy of the nitrogenase mechanism.

[1] Schindelin, H., Kisker, C., Schlessman, J., Howard, J., and Rees, D. (1997) Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Nature 387, 370-376.
[2] Schmid, B., Einsle, O., Chiu, H., Willing, A., Yoshida, M., Howard, J., Rees, D. (2002) Biochemistry 41,15557-15565.
[3] Einsle, O., Tezcan, F., Andrade, S., Schmid, B., Yoshida, M., Howard, J., Rees, D. Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the Fe-Mo cofactor. Science 297, 1696-1699.

Tuesday, March 1, 2011

Assignment #1

Nitrogenase Dimer


Fe-S Centers

Molybdenum-Fe-S Complex

Mg & ADP Binding