Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 

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Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway.

Xiao, X.Elsayed, S.S.Wu, C.van der Heul, H.U.Metsa-Ketela, M.Du, C.Prota, A.E.Chen, C.C.Liu, W.Guo, R.T.Abrahams, J.P.van Wezel, G.P.

(2020) ACS Chem Biol 15: 2529-2538

  • DOI: https://doi.org/10.1021/acschembio.0c00564
  • Primary Citation of Related Structures:  
    6YPZ, 6YQ0, 6YQ3, 6YQ6

  • PubMed Abstract: 

    Angucyclines are a structurally diverse class of actinobacterial natural products defined by their varied polycyclic ring systems, which display a wide range of biological activities. We recently discovered lugdunomycin ( 1 ), a highly rearranged polyketide antibiotic derived from the angucycline backbone that is synthesized via several yet unexplained enzymatic reactions. Here, we show via in vivo , in vitro , and structural analysis that the promiscuous reductase LugOII catalyzes both a C6 and an unprecedented C1 ketoreduction. This then sets the stage for the subsequent C-ring cleavage that is key to the rearranged scaffolds of 1 . The 1.1 Å structures of LugOII in complex with either ligand 8- O -Methylrabelomycin ( 4 ) or 8- O -Methyltetrangomycin ( 5 ) and of apoenzyme were resolved, which revealed a canonical Rossman fold and a remarkable conformational change during substrate capture and release. Mutational analysis uncovered key residues for substrate access, position, and catalysis as well as specific determinants that control its dual functionality. The insights obtained in this work hold promise for the discovery and engineering of other promiscuous reductases that may be harnessed for the generation of novel biocatalysts for chemoenzymatic applications.

  • Organizational Affiliation

    Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MonooxygenaseA [auth AAA],
B [auth BBB]
255Streptomyces sp. QL37Mutation(s): 0 
Gene Names: C5F59_12925
Find proteins for A0A2S6PN47 (Streptomyces sp. QL37)
Explore A0A2S6PN47 
Go to UniProtKB:  A0A2S6PN47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S6PN47
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth AAA],
G [auth BBB]
C21 H28 N7 O17 P3
P7Q (Subject of Investigation/LOI)
Query on P7Q

Download Ideal Coordinates CCD File 
D [auth AAA],
H [auth BBB]
C20 H16 O6
Query on EDO

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.969α = 90
b = 60.214β = 102.458
c = 88.308γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description