6YQ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report



Literature

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 

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

  • 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 rearran ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MonooxygenaseAAA, BBB255Streptomyces sp. QL37Mutation(s): 0 
Gene Names: C5F59_12925
Find proteins for A0A2S6PN47 (Streptomyces sp. QL37)
Explore A0A2S6PN47 
Go to UniProtKB:  A0A2S6PN47
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
AAA, BBB
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
P7Q
Query on P7Q

Download CCD File 
AAA, BBB
(3~{R})-8-methoxy-3-methyl-3,6-bis(oxidanyl)-2,4-dihydrobenzo[a]anthracene-1,7,12-trione
C20 H16 O6
LQIPGPPZCXJWKY-HXUWFJFHSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
AAA
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release