Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan

Acta Crystallogr F Struct Biol Commun. 2021 Jul 1;77(Pt 7):215-225. doi: 10.1107/S2053230X21006142. Epub 2021 Jul 30.

Abstract

The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand L-tryptophan (L-Trp) indicate that L-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with L-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it bears a disordered extension of about 20 residues, is accessible in the large solvent channels of the domain-swapped crystal form, as in the structures reported previously in this form for TrpR without N-terminal extensions. These findings inspire the exploration of L-Trp analogs and N-terminal modifications as labels to orient guest proteins that cannot otherwise be crystallized in the solvent channels of crystalline domain-swapped TrpR hosts for potential diffraction analysis.

Keywords: Val58Ile tryptophan repressor; crystalline protein gel; domain swapping; fragment-based screening; hostal system; ligand binding; molecular baits.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Crystallography, X-Ray / methods
  • Escherichia coli / genetics
  • Isoleucine / chemistry*
  • Isoleucine / genetics
  • Protein Domains / genetics
  • Protein Structure, Secondary
  • Repressor Proteins / chemistry*
  • Repressor Proteins / genetics
  • Tryptophan / chemistry*
  • Tryptophan / genetics
  • Valine / chemistry*
  • Valine / genetics
  • X-Ray Diffraction / methods*

Substances

  • Bacterial Proteins
  • Repressor Proteins
  • TRPR protein, E coli
  • Isoleucine
  • Tryptophan
  • Valine