Structure of the soluble domain of cytochrome c(552) from Paracoccus denitrificans in the oxidized and reduced states

J Mol Biol. 2000 Jan 21;295(3):667-78. doi: 10.1006/jmbi.1999.3382.

Abstract

The crystal structure of the soluble domain of the membrane bound cytochrome c(552) (cytochrome c(552)') from Paracoccus denitrificans was determined using the multiwavelength anomalous diffraction technique and refined at 1.5 A resolution for the oxidized and at 1. 4 A for the reduced state. This is the first high-resolution crystal structure of a cytochrome c at low ionic strength in both redox states. The atomic model allowed for a detailed assessment of the structural properties including the secondary structure, the heme geometry and interactions, and the redox-coupled structural changes. In general, the structure has the same features as that of known eukaryotic cytochromes c. However, the surface properties are very different. Cytochrome c(552)' has a large strongly negatively charged surface part and a smaller positively charged area around the solvent-exposed heme atoms. One of the internal water molecules conserved in all structures of eukaryotic cytochromes c is also present in this bacterial cytochrome c. It contributes to the interactions between the side-chain of Arg36 and the heme propionate connected to pyrrole ring A. Reduction of the oxidized crystals does not influence the conformation of cytochrome c(552)' in contrast to eukaryotic cytochromes c. The oxidized cytochrome c(552)', especially the region of amino acid residues 40 to 56, appears to be more flexible than the reduced one.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Cytochrome c Group / chemistry*
  • Heme / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Oxidation-Reduction
  • Paracoccus denitrificans / enzymology*
  • Protein Conformation
  • Solvents
  • Surface Properties

Substances

  • Cytochrome c Group
  • Solvents
  • cytochrome c553
  • Heme
  • cytochrome C-552

Associated data

  • PDB/1QL3
  • PDB/1QL4