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The Catalytic Mechanism of Biological Nitrogen Fixation

The enzyme nitrogenase was the target of my Ph.D. work with Peter Blöchl. Atmospheric N2 is the main natural source of nitrogen, which makes up about 10 % of the dry mass of biological matter. Nitrogenase, a bacterial enzyme, is able to convert atmospheric nitrogen into ammonia and thus to break the strongest chemical bond in nature. The reaction it catalyzes is

N2 + 8 e + 8 H+ + 16 ATP → 16 ADP + 16 Pi + 2 NH3 + H2

Although the structure of the protein had been resolved almost ten years ago, the reaction mechanism is still in the dark. The active center of the enzyme (FeMo-cofactor) is a cluster containing one molybdenum atom and seven iron atoms connected by sulfur bridges. A central ligand in the cage, most probably nitrogen, has only been discovered in 2002 (Science 197, 1696 (2002)). Thus although there are a lot of experimental data available on this system, they alone are not sufficient for unraveling the reaction mechanism. Theory is required.

The system is a real challenge for a theoretician as the complicated spin structure of the FeMo-cofactor (shown on the right) is difficult – if not impossible – to describe with standard methods. Therefore we used the PAW method with a noncollinear description of the spin density. This avoids metastable minima and thus increases the reliability of the calculations.

We investigated the resting state of the FeMo-cofactor, reductions and protonations, and nitrogen binding. We found two stable binding modes, shown on the right [2]. The FeMo-cofactor was found to be flexible: a sulfur bridge opens during N2 binding.

reaction cycle of nitrogenase

We worked out a model for the complete reaction mechanism of biological nitrogen reduction [3,9]. An overview, similar to the one in Ref. [3], is shown above. The energetically most difficult step is the first protonation of N2 bound to FeMo-cofactor [1]. As it can already be seen from the nitrogen binding modes, the central ligand plays an important role as it can offer a variable number of bonds to its iron neighbors. Therfore it allows efficient binding of differently-sized intermediates.

The mechanism we found explains many experimental facts. In order to verify it, we also investigated the experimentally observed hydrogen production. Additionally, investigations on acetylene (C2H2) interacting with the FeMo-cofactor explain how C2H2 and N2 inhibit each other [4].

nitrogenase resting state
nitrogenase axial N2 bonding mode nitrogenase bridged N2 binding mode
   © 2003–08 by Johannes Kästner   ·   last modified Nov 11, 2008