P450cin active site water: implications for substrate binding and solvent accessibility

Biochemistry. 2013 Jul 30;52(30):5039-50. doi: 10.1021/bi4006946. Epub 2013 Jul 18.

Abstract

In P450cin, Tyr81, Asp241, Asn242, two water molecules, and the substrate participate in a complex H-bonded network. The role of this H-bonded network in substrate binding and catalysis has been probed by crystallography, spectroscopy, kinetics, isothermal titration calorimetry (ITC), and molecular dynamics. For the Y81F mutant, the substrate binds about 20-fold more weakly and Vmax decreases by about 30% in comparison to WT. The enhanced susceptibility of the heme to H₂O₂-mediated destruction in Y81F suggests that this mutant favors the open, low-spin conformational state. Asn242 H-bonds directly with the substrate, and replacing this residue with Ala results in water taking the place of the missing Asn side chain. This mutant exhibits a 70% decrease in activity. Crystal structures and molecular dynamics simulations of substrate-bound complexes show that the solvent has more ready access to the active site, especially for the N242A mutant. This accounts for about a 64% uncoupling of electron transfer from substrate hydroxylation. These data indicate the importance of the interconnected water network on substrate binding and on the open/closed conformational equilibrium, which are both critically important for maintaining high-coupling efficiency.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Asparagine / chemistry
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Catalytic Domain
  • Citrobacter / enzymology*
  • Cyclohexanols / chemistry
  • Cyclohexanols / metabolism
  • Cytochrome P-450 Enzyme System / chemistry
  • Cytochrome P-450 Enzyme System / genetics
  • Cytochrome P-450 Enzyme System / metabolism*
  • Electron Transport
  • Eucalyptol
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Hydroxylation
  • Kinetics
  • Models, Molecular*
  • Monoterpenes / chemistry
  • Monoterpenes / metabolism
  • Mutagenesis, Site-Directed
  • Mutant Proteins / chemistry
  • Mutant Proteins / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Substrate Specificity
  • Surface Properties
  • Water / chemistry
  • Water / metabolism*

Substances

  • Bacterial Proteins
  • Cyclohexanols
  • Monoterpenes
  • Mutant Proteins
  • Recombinant Proteins
  • Water
  • Asparagine
  • Cytochrome P-450 Enzyme System
  • cytochrome P-450 176A
  • Eucalyptol

Associated data

  • PDB/4L6G
  • PDB/4L77
  • PDB/4LHT