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Homology modelling of the Frankia nitrogenase iron protein

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Abstract

The NifH protein contains an iron-sulfur cluster performing different functions during nitrogen fixation. Frankia is an actinomycete, entering into symbiotic association with a number of dicotyledonous plants and fixing nitrogen. The structure of the Frankia NifH protein was determined using homology modelling technique. Metal binding sites and functionally important regions of the protein were analyzed. Thiol ligands and active sites help in protein functioning and conformations. Structurally important nests were recognized. Clefts and cavities contain biologically important residues. Site-directed mutagenesis results reveal that mutations in functional residues hamper nitrogen fixation. The structure is rigid with an accessible surface for solvents. The structure is reliable offering insights into the 3D structural framework as well as structure-function relation of NifH protein.

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Acknowledgements

The authors are grateful to the Department of Biotechnology, Government of India, for providing financial help in setting up Bioinformatics Centre, in the Department of Botany, University of North Bengal. A Sen acknowledges the receipt of Department of Biotechnology, Overseas Associateship. The authors thank Prof. Philip Normand for helpful suggestions.

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Authors and Affiliations

  1. NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734013, India

    Arnab Sen, Saubashya Sur & Subarna Thakur

  2. Department of Microbiology, University of New Hampshire, Durham, 03824, NH, USA

    Louis S. Tisa

  3. Chemiinformatics Bioinformatics Laboratory, Department of Chemistry, Raiganj (University) College, Raiganj, 733134, India

    Asim Kr. Bothra & Uttam Kr. Mondal

Authors
  1. Arnab Sen
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  2. Saubashya Sur
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  3. Louis S. Tisa
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  4. Asim Kr. Bothra
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  5. Subarna Thakur
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  6. Uttam Kr. Mondal
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Corresponding author

Correspondence to Asim Kr. Bothra.

Electronic supplementary material

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Supplementary Table 1

Summary of the characteristics of the nitrogenase iron protein from Frankia sp. EANIpec. Functional region mentioned in the table refers to the ligand binding region. (DOC 36 kb)

Supplementary Figure A

Clefts and cavities present on the surface of the nitrogenase iron proteins from Frankia (DOC 195 kb)

Supplementary Figure B

Energy plots of the nitrogenase iron proteins from Frankia strains. Residue energies averaged over a sliding window are plotted as a function of the central residue in the window (DOC 70 kb)

Supplementary Figure C

Ramachandran plot of the nitrogenase iron proteins from Frankia showing the residue backbone conformations for the modelled proteins (DOC 410 kb)

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Sen, A., Sur, S., Tisa, L.S. et al. Homology modelling of the Frankia nitrogenase iron protein. Symbiosis 50, 37–44 (2010). https://doi.org/10.1007/s13199-009-0035-9

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