Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW

Biochem Biophys Res Commun. 2017 Sep 16;491(2):409-415. doi: 10.1016/j.bbrc.2017.07.088. Epub 2017 Jul 15.

Abstract

LysK is an M20 peptidase family enzyme that hydrolyzes the isopeptide bond between the carrier protein LysW and lysine in order to release lysine, which is the last step of lysine biosynthesis in Thermus thermophilus. In the present study, we determined the crystal structure of LysK in complex with lysine at a resolution of 2.4 Å. The α-amino group of the bound lysine was oriented toward the catalytic center, which was composed of the residues coordinating divalent metal ions for the hydrolysis of the isopeptide bond. An 11 Å-long path was observed from the active site binding lysine to the protein surface, which may be responsible for recognizing the C-terminal extension domain of LysW with the conserved EDWGE sequence. A positively-charged surface region was detected around the exit of the path, similar to other lysine biosynthetic enzymes using LysW as the carrier protein. Mutational studies of the surface residues provided a plausible model for the electrostatic interaction with LysW.

Keywords: Amino-group carrier protein; Crystal structure; LysK; M20 metallopeptidase; Thermus thermophilus.

MeSH terms

  • Amidohydrolases / chemistry*
  • Amidohydrolases / genetics
  • Amidohydrolases / metabolism
  • Amino Acid Sequence
  • Amino Acid Substitution
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • Cloning, Molecular
  • Conserved Sequence
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Kinetics
  • Lysine / biosynthesis*
  • Lysine / chemistry
  • Models, Molecular
  • Mutation
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Static Electricity
  • Substrate Specificity
  • Thermus thermophilus / chemistry*
  • Thermus thermophilus / enzymology

Substances

  • Bacterial Proteins
  • Carrier Proteins
  • Recombinant Proteins
  • Amidohydrolases
  • LysK protein, Thermus thermophilus
  • Lysine