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Related Concept Videos

Inorganic Nitrogen Assimilation01:22

Inorganic Nitrogen Assimilation

Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme nitrate reductase...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function

James B Howard1, Katerina J Kechris, Douglas C Rees

  • 1Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America ; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America.

Plos One
|September 11, 2013
PubMed
Summary

Natural selection preserves critical amino acids in nitrogen fixation proteins. Analyzing 95 homologous sequences identified core residues essential for nitrogenase function across different genotypes.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Microbial Genetics and Evolution
  • Nitrogen Fixation Research

Background:

  • Amino acid residues crucial for protein structure-function are evolutionarily conserved.
  • Identifying these conserved residues in nitrogen fixation proteins (Component 1 α- and β-subunits) is key to understanding their function.
  • Nitrogen fixation involves diverse genotypes (anf, nif, vnf) encoding proteins with varied cofactor metal sites.

Purpose of the Study:

  • To identify evolutionarily conserved amino acid residues critical for nitrogenase function.
  • To analyze sequence variations across different nitrogen fixation genotypes (anf, nif, vnf).
  • To provide a basis for future structural and mutagenesis studies of nitrogenase.

Main Methods:

  • Alignment of 95 homologous protein sequences from diverse microbial species and nitrogen fixation genotypes.
  • Sequence analysis to identify invariant and single variant residues after adjusting for length, insertions, and deletions.
  • Grouping of aligned sequences into six categories (Anf, Vnf, Nif I-IV) based on genetic origin and conserved residues.

Main Results:

  • Over 85% of the sequences co-aligned across the three genotypes after adjustments.
  • Identified invariant and single variant residues as 'core' residues essential for nitrogenase function.
  • Found that 14 of 19 residues in the cofactor pocket are invariant or single variant; five are highly variable and located away from functional centers.

Conclusions:

  • The study identified previously unrecognized critical residues for nitrogenase function.
  • Specific subsets of invariant residues can help identify the gene of origin (anf, nif, vnf).
  • The findings provide a foundation for detailed three-dimensional structure analysis and targeted mutagenesis studies.