5L3Z

polyketide ketoreductase SimC7 - binary complex with NADP+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Substrate-Assisted Catalysis in Polyketide Reduction Proceeds via a Phenolate Intermediate.

Schafer, M., Stevenson, C.E., Wilkinson, B., Lawson, D.M., Buttner, M.J.

(2016) Cell Chem Biol 23: 1091-1097

  • DOI: 10.1016/j.chembiol.2016.07.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • SimC7 is a polyketide ketoreductase involved in biosynthesis of the angucyclinone moiety of the gyrase inhibitor simocyclinone D8 (SD8). SimC7, which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, catalyzes reduction of the C-7 ...

    SimC7 is a polyketide ketoreductase involved in biosynthesis of the angucyclinone moiety of the gyrase inhibitor simocyclinone D8 (SD8). SimC7, which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, catalyzes reduction of the C-7 carbonyl of the angucyclinone, and the resulting hydroxyl is essential for antibiotic activity. SimC7 shares little sequence similarity with characterized ketoreductases, suggesting it might have a distinct mechanism. To investigate this possibility, we determined the structures of SimC7 alone, with NADP(+), and with NADP(+) and the substrate 7-oxo-SD8. These structures show that SimC7 is distinct from previously characterized polyketide ketoreductases, lacking the conserved catalytic triad, including the active-site tyrosine that acts as central acid-base catalyst in canonical SDR proteins. Taken together with functional analyses of active-site mutants, our data suggest that SimC7 catalyzes a substrate-assisted, two-step reaction for reduction of the C-7 carbonyl group involving intramolecular transfer of a substrate-derived proton to generate a phenolate intermediate.

    Organizational Affiliation: 

    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
polyketide ketoreductase SimC7
A
304Streptomyces antibioticusMutation(s): 0 
Gene Names: simC7
Find proteins for G9VYV4 (Streptomyces antibioticus)
Go to UniProtKB:  G9VYV4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.230α = 90.00
b = 52.230β = 90.00
c = 214.000γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I002197/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomDoctoral Training Partnership

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence