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Classifying the metal dependence of uncharacterized nitrogenases
Shawn E McGlynn1, Eric S Boyd, John W Peters
1Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA.
Frontiers in Microbiology
|February 27, 2013
Summary
Newly discovered nitrogenase enzymes in archaea likely use molybdenum-iron-sulfur (Fe-Mo-co) cofactors, similar to known nitrogenase enzymes. This suggests structural evolution driven by metal utilization in ancient anoxic environments.
Area of Science:
- Biochemistry
- Enzymology
- Structural Biology
Background:
- Nitrogenase enzymes catalyze dinitrogen (N(2)) to ammonia (NH(3)) conversion using complex iron-sulfur (Fe-S) cofactors.
- Known nitrogenases include molybdenum-iron (MoFe, Nif), vanadium-iron (VFe, Vnf), and iron-only (Fe-only, Anf) forms, differing in catalytic rates and specificity.
- Uncharacterized nitrogenase homologs found in archaeal methanotrophs and methanogens do not align with previously classified nitrogenases.
Purpose of the Study:
- To investigate the metal cofactors of uncharacterized nitrogenase homologs.
- To understand the structural basis for metal utilization in nitrogenase evolution.
Main Methods:
- Predicted three-dimensional structures of nitrogenase active site subunits (NifD, VnfD, AnfD).
- Comparative analysis of structural similarities using dendrograms.
- Examination of amino acid variations in the active site environment.
Main Results:
- Nitrogenase homologs cluster phylogenetically based on their heterometal cofactor content.
- Uncharacterized nitrogenase D homologs structurally align with NifD (MoFe nitrogenase).
- Active site analysis reveals amino acid similarities between uncharacterized nitrogenases and NifD.
Conclusions:
- Uncharacterized nitrogenase homologs likely bind the molybdenum-iron-sulfur cluster (Fe-Mo-co).
- Enzyme structure has evolved in response to specific metal cofactor utilization.
- Diversification of metal utilization in nitrogenases likely originated in anoxic habitats.
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