New insights into structure-function relationships in nitrogenase: A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein

J Mol Biol. 1999 Oct 1;292(4):871-91. doi: 10.1006/jmbi.1999.3107.

Abstract

The X-ray crystal structure of Klebsiella pneumoniae nitrogenase component 1 (Kp1) has been determined and refined to a resolution of 1.6 A, the highest resolution reported for any nitrogenase structure. Models derived from three 1.6 A resolution X-ray data sets are described; two represent distinct oxidation states, whilst the third appears to be a mixture of both oxidized and reduced states (or perhaps an intermediate state). The structures of the protein and the iron-molybdenum cofactor (FeMoco) appear to be largely unaffected by the redox status, although the movement of Ser beta90 and a surface helix in the beta subunit may be of functional significance. By contrast, the 8Fe-7S P-cluster undergoes discrete conformational changes involving the movement of two iron atoms. Comparisons with known component 1 structures reveal subtle differences in the FeMoco environment, which could account for the lower midpoint potential of this cluster in Kp1. Furthermore, a non-proline- cis peptide bond has been identified in the alpha subunit that may have a functional role. It is within 10 A of the FeMoco and may have been overlooked in other component 1 models. Finally, metal-metal and metal-sulphur distances within the metal clusters agree well with values derived from EXAFS studies, although they are generally longer than the values reported for the closely related protein from Azotobacter vinelandii. A number of bonds between the clusters and their ligands are distinctly longer than the EXAFS values, in particular, those involving the molybdenum atom of the FeMoco.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • Electrons
  • Iron / chemistry
  • Iron / metabolism
  • Klebsiella pneumoniae / enzymology*
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Molybdenum / chemistry
  • Molybdenum / metabolism
  • Molybdoferredoxin / chemistry*
  • Molybdoferredoxin / metabolism
  • Nitrogenase / chemistry*
  • Nitrogenase / metabolism
  • Oxidation-Reduction
  • Proline / chemistry
  • Proline / metabolism
  • Protein Conformation
  • Structure-Activity Relationship
  • Sulfur / chemistry
  • Sulfur / metabolism

Substances

  • Ligands
  • Molybdoferredoxin
  • Sulfur
  • Molybdenum
  • Proline
  • Iron
  • Nitrogenase

Associated data

  • PDB/1QGU
  • PDB/1QH1
  • PDB/1QH8