Structural insights into the substrate selectivity of acyl-CoA transferase

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Structural insights into the substrate selectivity of alpha-oxoamine synthases from marine Vibrio sp. QWI-06.

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.

(2022) Colloids Surf B Biointerfaces 210: 112224-112224

  • DOI: https://doi.org/10.1016/j.colsurfb.2021.112224
  • Primary Citation of Related Structures:  
    7V58, 7V5I

  • 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.

  • Organizational Affiliation

    Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan. Electronic address: hychang5@nycu.edu.tw.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-amino-3-ketobutyrate coenzyme A ligase
A, B
400Vibrio proteolyticus NBRC 13287Mutation(s): 0 
Gene Names: kblVPR01S_15_00210
Find proteins for U3BPN5 (Vibrio proteolyticus NBRC 13287)
Explore U3BPN5 
Go to UniProtKB:  U3BPN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3BPN5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Query on MES

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D [auth A],
E [auth A],
H [auth B],
I [auth B]
C6 H13 N O4 S
Query on SO4

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F [auth A],
G [auth A],
J [auth B]
O4 S
GLY (Subject of Investigation/LOI)
Query on GLY

Download Ideal Coordinates CCD File 
C2 H5 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.724α = 90
b = 122.63β = 90
c = 136.462γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-2311-B-010-007-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description