Structural consequences of an amino acid deletion in the B1 domain of protein G

Proteins. 2000 Nov 15;41(3):323-33. doi: 10.1002/1097-0134(20001115)41:3<323::aid-prot50>;2-r.


We describe the NMR structure of a deletion mutant of the B1 IgG-binding domain from Group G Streptococcus. The deletion occurs within the last beta-strand of the protein, where it may potentially have a deleterious effect on the stability of the protein if the protein were not able to conformationally adjust to the perturbation. In particular, the deletion changes the registry of the final three residues in the sheet, forcing a polar Thr to be buried in the interior of the protein and exposing a hydrophobic Val to solvent. The deletion could also potentially create a large cavity in the beta-sheet and force the alpha- and gamma-carboxylates of the C-terminal Glu residue into a partially buried region of the sheet. The structure of the mutant illustrates how the conformation of the protein adjusts to the deletion, thereby mitigating some of the potentially deleterious consequences. Although the elements of secondary structure are retained between the mutant and the wt domain, there are multiple small adjustments in the segments connecting secondary structure elements. In particular, a hydrogen bond between the Glu57 carboxylates and two main chain amides is introduced that alters the conformation in the loop connecting the helix to strand 3. In addition, to minimize hydrophobic surface exposure, the turn connecting strands 1 and 2 folds toward the core so that the molecular volume is decreased.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Circular Dichroism
  • Computer Simulation
  • Models, Molecular
  • Molecular Sequence Data
  • Motion
  • Mutation*
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptide Fragments / chemistry
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Receptors, IgG / chemistry*
  • Receptors, IgG / genetics
  • Sequence Deletion
  • Solutions
  • Thermodynamics


  • Bacterial Proteins
  • IgG Fc-binding protein, Streptococcus
  • Peptide Fragments
  • Receptors, IgG
  • Solutions