Precise Probing of Residue Roles by NRPS Code Swapping: Mutation, Enzymatic Characterization, Modeling, and Substrate Promiscuity of Aryl Acid Adenylation Domains

Biochemistry. 2020 Feb 4;59(4):351-363. doi: 10.1021/acs.biochem.9b00748. Epub 2020 Jan 15.

Abstract

Aryl acids are most commonly found in iron-scavenging siderophores but are not limited to them. The nonribosomal peptide synthetase (NRPS) codes of aryl acids remain poorly elucidated relative to those of amino acids. Here, we defined more precisely the role of active-site residues in aryl acid adenylation domains (A-domains) by gradually grafting the NRPS codes used for salicylic acid (Sal) into an archetypal aryl acid A-domain, EntE [specific for the substrate 2,3-dihydroxybenzoic acid (DHB)]. Enzyme kinetics and modeling studies of these EntE variants demonstrated that the NRPS code residues at positions 236, 240, and 339 collectively regulate the substrate specificity toward DHB and Sal. Furthermore, the EntE variants exhibited the ability to activate the non-native aryl acids 3-hydroxybenzoic acid, 3-aminobenzoic acid, 3-fluorobenzoic acid, and 3-chlorobenzoic acid. These studies enhance our knowledge of the NRPS codes of aryl acids and could be exploited to reprogram aryl acid A-domains for non-native aryl acids.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / chemistry
  • Adenosine Monophosphate / metabolism*
  • Amino Acid Sequence
  • Amino Acids / genetics
  • Catalytic Domain
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Hydroxybenzoates / chemistry
  • Ligases / chemistry*
  • Ligases / metabolism
  • Mutation
  • Peptide Synthases / chemistry
  • Peptide Synthases / metabolism*
  • Salicylic Acid / chemistry
  • Siderophores / chemistry
  • Substrate Specificity

Substances

  • Amino Acids
  • Escherichia coli Proteins
  • Hydroxybenzoates
  • Siderophores
  • Adenosine Monophosphate
  • 2,3-dihydroxybenzoic acid
  • Ligases
  • Peptide Synthases
  • non-ribosomal peptide synthase
  • 2,3-dihydroxybenzoate-AMP ligase, E coli
  • phenolic acid
  • Salicylic Acid