6YPZ | pdb_00006ypz

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.165 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.147 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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 15: 2529-2538

  • DOI: https://doi.org/10.1021/acschembio.0c00564
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 56.04 kDa 
  • Atom Count: 4,481 
  • Modeled Residue Count: 505 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MonooxygenaseA [auth AAA],
B [auth BBB]
255Streptomyces sp. QL37Mutation(s): 0 
Gene Names: C5F59_12925

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
C [auth AAA],
M [auth BBB]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
O [auth BBB],
R [auth BBB]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
H [auth AAA]
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
N [auth BBB],
P [auth BBB],
Q [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.165 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.147 (DCC) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.828α = 90
b = 59.965β = 102.513
c = 88.428γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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