Structural Determinants Defining the Allosteric Inhibition of an Essential Antibiotic Target

• Published in: Structure (London) Vol. 24; no. 8; pp. 1282 - 1291
• Main Authors: Soares da Costa, Tatiana P., Desbois, Sebastien, Dogovski, Con, Gorman, Michael A., Ketaren, Natalia E., Paxman, Jason J., Siddiqui, Tanzeela, Zammit, Leanne M., Abbott, Belinda M., Robins-Browne, Roy M., Parker, Michael W., Jameson, Geoffrey B., Hall, Nathan E., Panjikar, Santosh, Perugini, Matthew A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 02-08-2016
• Subjects: Allosteric Regulation; Allosteric Site; Amino Acid Sequence; Binding Sites; Cloning, Molecular; Crystallography, X-Ray; Escherichia coli - enzymology; Escherichia coli - genetics; Feedback, Physiological; Gene Expression; Hydro-Lyases - chemistry; Hydro-Lyases - genetics; Hydro-Lyases - metabolism; Kinetics; Legionella pneumophila - enzymology; Legionella pneumophila - genetics; Lysine - chemistry; Lysine - metabolism; Models, Molecular; 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; Streptococcus pneumoniae - enzymology; Streptococcus pneumoniae - genetics; Substrate Specificity
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2016.05.019

Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine biosynthesis pathway of bacteria. The pathway can be regulated by feedback inhibition of DHDPS through the allosteric binding of the end product, lysine. The current dogma states that DHDPS from Gram-negative bacteria are inhibited by lysine but orthologs from Gram-positive species are not. The 1.65-Å resolution structure of the Gram-negative Legionella pneumophila DHDPS and the 1.88-Å resolution structure of the Gram-positive Streptococcus pneumoniae DHDPS bound to lysine, together with comprehensive functional analyses, show that this dogma is incorrect. We subsequently employed our crystallographic data with bioinformatics, mutagenesis, enzyme kinetics, and microscale thermophoresis to reveal that lysine-mediated inhibition is not defined by Gram staining, but by the presence of a His or Glu at position 56 (Escherichia coli numbering). This study has unveiled the molecular determinants defining lysine-mediated allosteric inhibition of bacterial DHDPS.
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•Crystal structure of L. pneumophila DHDPS and lysine-bound S. pneumoniae DHDPS•DHDPS allosteric inhibition is not defined by Gram staining•Glu or His at position 56 in DHDPS defines lysine binding•DHDPS enzymes with Lys or Arg at position 56 are not inhibited by lysine
In some bacteria, lysine biosynthesis is regulated by lysine-mediated allosteric inhibition of the enzyme dihydrodipicolinate synthase (DHDPS). Soares da Costa et al. show that position 56 (E. coli numbering) defines DHDPS allostery, dispelling the current dogma that regulation is based on Gram staining.