NMR Structure of Cysteinyl-Phosphorylated Enzyme IIB of the N,N'-diacetylchitobiose-specific Phosphoenolpyruvate-Dependent Phosphotransferase System of Escherichia Coli

J Mol Biol. 2001 May 18;308(5):993-1009. doi: 10.1006/jmbi.2001.4623.

Abstract

The determination by NMR of the solution structure of the phosphorylated enzyme IIB (P-IIB(Chb)) of the N,N'-diacetylchitobiose-specific phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli is presented. Most of the backbone and side-chain resonances were assigned using a variety of mostly heteronuclear NMR experiments. The remaining resonances were assigned with the help of the structure calculations.NOE-derived distance restraints were used in distance geometry calculations followed by molecular dynamics and simulated annealing protocols. In addition, combinations of ambiguous restraints were used to resolve ambiguities in the NOE assignments. By combining sets of ambiguous and unambiguous restraints into new ambiguous restraints, an error function was constructed that was less sensitive to information loss caused by assignment uncertainties. The final set of structures had a pairwise rmsd of 0.59 A and 1.16 A for the heavy atoms of the backbone and side-chains, respectively. Comparing the P-IIB(Chb) solution structure with the previously determined NMR and X-ray structures of the wild-type and the Cys10Ser mutant shows that significant differences between the structures are limited to the active-site region. The phosphoryl group at the active-site cysteine residue is surrounded by a loop formed by residues 10 through 16. NOE and chemical shift data suggest that the phosphoryl group makes hydrogen bonds with the backbone amide protons of residues 12 and 15. The binding mode of the phosphoryl group is very similar to that of the protein tyrosine phosphatases. The differences observed are in accordance with the presumption that IIB(Chb) has to be more resistant to hydrolysis than the protein tyrosine phosphatases. We propose a proton relay network by which a transfer occurs between the cysteine SH proton and the solvent via the hydroxyl group of Thr16.

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • Cysteine / metabolism*
  • Disaccharides / metabolism*
  • Escherichia coli / enzymology*
  • Hydrogen Bonding
  • Models, Molecular
  • Mutation
  • Nuclear Magnetic Resonance, Biomolecular*
  • Phosphoenolpyruvate Sugar Phosphotransferase System / chemistry*
  • Phosphoenolpyruvate Sugar Phosphotransferase System / genetics
  • Phosphoenolpyruvate Sugar Phosphotransferase System / metabolism*
  • Phosphorylation
  • Protein Structure, Secondary
  • Protons
  • Solvents
  • Substrate Specificity
  • Thermodynamics

Substances

  • Disaccharides
  • Protons
  • Solvents
  • N,N-diacetylchitobiose
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphoenolpyruvate-cellobiose phosphotransferase
  • Cysteine

Associated data

  • PDB/1E2B
  • PDB/1H9C
  • PDB/1IIB