7V5I

Structural insights into the substrate selectivity of acyl-CoA transferase

Summary for 7V5I

• Entry DOI: 10.2210/pdb7v5i/pdb
• Descriptor: 2-amino-3-ketobutyrate coenzyme A ligase, PYRIDOXAL-5'-PHOSPHATE (3 entities in total)
• Functional Keywords: acyltransferase, pyridoxal phosphate, sphingolipids, transferase
• Biological source: Vibrio proteolyticus NBRC 13287
• Total number of polymer chains: 4
• Total formula weight: 175907.16

Authors

Chang, H.Y.,Ko, T.P. (deposition date: 2021-08-17, release date: 2021-12-29, Last modification date: 2023-11-29)

Primary citation

Chang, H.Y.,Lo, L.H.,Lan, Y.H.,Hong, M.X.,Chan, Y.T.,Ko, T.P.,Huang, Y.R.,Cheng, T.H.,Liaw, C.C.
Structural insights into the substrate selectivity of alpha-oxoamine synthases from marine Vibrio sp. QWI-06.
Colloids Surf B Biointerfaces, 210:112224-112224, 2022

PubMed Abstract: Pyridoxal phosphate (PLP)-dependent α-oxoamine synthases are generally believed to be responsible for offloading and elongating polyketides or catalyzing the condensation of amino acids and acyl-CoA thioester substrates, such as serine into sphingolipids and cysteate into sulfonolipids. Previously, we discovered vitroprocines, which are tyrosine- and phenylalanine-polyketide derivatives, as potential new antibiotics from the genus Vibrio. Using bioinformatics analysis, we identified putative genes of PLP-dependent enzyme from marine Vibrio sp. QWI-06, implying a capability to produce amino-polyketide derivatives. One of these genes was cloned, and the recombinant protein, termed Vibrio sp. QWI-06 α-oxoamine synthases-1 (VsAOS1), was overexpressed for structural and biochemical characterization. The crystal structure of the dimeric VsAOS1 was determined at 1.8-Å resolution in the presence of L-glycine. The electron density map indicated a glycine molecule occupying the pyridoxal binding site in one monomer, suggesting a snapshot of the initiation process upon the loading of amino acid substrate. In mass spectrometry analysis, VsAOS1 strictly acted to condense L-glycine with C12 or C16 acyl-CoA, including unsaturated acyl analog. Furthermore, a single residue replacement of VsAOS1 (G243S) allowed the enzyme to generate sphingoid derivative when L-serine and lauroyl-CoA were used as substrates. Our data elucidate the mechanism of substrate binding and selectivity by the VsAOS1 and provide a thorough understanding of the molecular basis for the amino acid preference of AOS members.

PubMed: 34838420
DOI: 10.1016/j.colsurfb.2021.112224

Experimental method

X-RAY DIFFRACTION (3.08 Å)