Structural basis for acyl acceptor specificity in the achromobactin biosynthetic enzyme AcsD |
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Authors: | Schmelz Stefan Botting Catherine H Song Lijiang Kadi Nadia F Challis Gregory L Naismith James H |
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Institution: | 1 Scottish Structural Proteomics Facility and Centre for Biomolecular Sciences, The University of St Andrews, Scotland KY16 9ST, UK2 Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK |
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Abstract: | Siderophores are known virulence factors, and their biosynthesis is a target for new antibacterial agents. A non-ribosomal peptide synthetase-independent siderophore biosynthetic pathway in Dickeya dadantii is responsible for production of the siderophore achromobactin. The D. dadantii achromobactin biosynthesis protein D (AcsD) enzyme has been shown to enantioselectively esterify citric acid with l-serine in the first committed step of achromobactin biosynthesis. The reaction occurs in two steps: stereospecific activation of citric acid by adenylation, followed by attack of the enzyme-bound citryl adenylate by l-serine to produce the homochiral ester. We now report a detailed characterization of the substrate profile and mechanism of the second (acyl transfer) step of AcsD enzyme. We demonstrate that the enzyme catalyzes formation of not only esters but also amides from the citryl-adenylate intermediate. We have rationalized the substrate utilization profile for the acylation reaction by determining the first X-ray crystal structure of a product complex for this enzyme class. We have identified the residues that are important for both recognition of l-serine and catalysis of ester formation. Our hypotheses were tested by biochemical analysis of various mutants, one of which shows a reversal of specificity from the wild type with respect to non-natural substrates. This change can be rationalized on the basis of our structural data. That this change in specificity is accompanied by no loss in activity suggests that AcsD and other members of the non-ribosomal peptide synthetase-independent siderophore superfamily may have biotransformation potential. |
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Keywords: | AcsD achromobactin biosynthesis protein D NRPS non-ribosomal peptide synthetase NIS NRPS-independent siderophore MS mass spectrometry HRMS high-resolution mass spectrometry MS/MS tandem mass spectrometry CEDA (3&prime S)-N-citryl-ethylenediamine PDB Protein Data Bank |
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