8HK0

Crystal structure of Fic32-33 complex from Streptomyces ficellus NRRL 8067


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Literature

Oxidase Heterotetramer Completes 1-Azabicyclo[3.1.0]hexane Formation with the Association of a Nonribosomal Peptide Synthetase.

Cheng, Y.Yi, X.Zhang, Y.He, Q.Chen, D.Cao, W.Fang, P.Liu, W.

(2023) J Am Chem Soc 145: 8896-8907

  • DOI: https://doi.org/10.1021/jacs.2c12507
  • Primary Citation of Related Structures:  
    8GS1, 8HK0

  • PubMed Abstract: 

    Ficellomycin, azinomycins, and vazabitide A are nonribosomal peptide natural products characterized by an amino acid unit that contains a similar 1- a za b i c yclo[3.1.0] h exane (ABCH) pharmacophore. This unit is derived from d i a mino- d ihydroxy- h eptanic acid (DADH); however, the process through which linear DADH is cyclized to furnish an ABCH ring system remains poorly understood. Based on the reconstitution of the route of the ABCH-containing unit by blending genes/enzymes involved in the biosynthesis of ficellomycin and azinomycins, we report that ABCH formation is completed by an oxidase heterotetramer with the association of a nonribosomal peptide synthetase (NRPS). The DADH precursor was prepared in Escherichia coli to produce a conjugate subjected to in vitro enzymatic hydrolysis for offloading from an amino-group carrier protein. To furnish an aziridine ring, DADH was processed by C7-hydroxyl sulfonation and sulfate elimination-coupled cyclization. Further cyclization leading to an azabicyclic hexane pharmacophore was proved to occur in the NRPS, where the oxidase heterotetramer functions in trans and catalyzes α,β-dehydrogenation to initiate the formation of a fused five-membered nitrogen heterocycle. The identity of ABCH was validated by utilization of the resultant ABCH-containing unit in the total biosynthesis of ficellomycin. Biochemical characterization, crystal structure, and site-specific mutagenesis rationalize the catalytic mechanism of the unusual oxidase heterotetramer.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DehydrogenaseA [auth C],
B [auth D]
380Streptomyces ficellusMutation(s): 0 
Gene Names: EIZ62_06145
UniProt
Find proteins for A0A1W5T2G8 (Streptomyces ficellus)
Explore A0A1W5T2G8 
Go to UniProtKB:  A0A1W5T2G8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W5T2G8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenaseC [auth A],
D [auth B]
384Streptomyces ficellusMutation(s): 0 
Gene Names: EIZ62_06140
UniProt
Find proteins for A0A1W5T3Z2 (Streptomyces ficellus)
Explore A0A1W5T3Z2 
Go to UniProtKB:  A0A1W5T3Z2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W5T3Z2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.08α = 90
b = 137.08β = 90
c = 148.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21778064
National Natural Science Foundation of China (NSFC)China21977107

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references