PROSITE documentation PDOC00580

NifH/frxC family signatures and profile

Nitrogenase (EC 1.18.6.1) [1] is the enzyme system responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 1 which contains the active site for the reduction of nitrogen to ammonia and component 2 (also called the iron protein).

Component 2 is a homodimer of a protein (gene nifH) which binds a single 4Fe-4S iron sulfur cluster [2]. In the nitrogen fixation process nifH is first reduced by a protein such as ferredoxin; the reduced protein then transfers electrons to component 1 with the concomitant consumption of ATP.

Crystal structure of the nitrogenase iron protein has been solved (see <PDB:1NIP>)[2], and revealed that it is composed of two subunits, each folded as a single α/β type domain and connected at one surface by the 4Fe:4S cluster. The shape of the overall fold could be described as either an iron butterfly or an iron lung, with the cluster representing the head or the heart respectively. At the core of each subunit is an eight-stranded β sheet (with seven of the eight β strands oriented in parallel fashion), flanked by nine α helices. This fold is a common motif found in nucleotide-binding proteins [2].

A number of proteins are known to be evolutionary related to nifH. These proteins are:

• Chloroplast encoded chlL (or frxC) protein [3]. ChlL is encoded on the chloroplast genome of some plant species, its exact function is not known, but it could act as an electron carrier in the conversion of protochlorophyllide to chlorophyllide.
• Photosynthetic bacteria proteins bchL and bchX [4]. These proteins are also likely to play a role in chlorophyll synthesis.

There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster. We have developed two signature patterns that correspond to the regions around these cysteines, and a profile which cover all the conserved regions.