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 
  • R-Value Observed: 0.183 

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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:  
    5L3Z, 5L40, 5L45, 5L4L

  • 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 carbonyl of the angucyclinone, and the resulting hydroxyl is essential for antibiotic activity ...

    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. Electronic address: mark.buttner@jic.ac.uk.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
polyketide ketoreductase SimC7A304Streptomyces antibioticusMutation(s): 0 
Gene Names: simC7
UniProt
Find proteins for G9VYV4 (Streptomyces antibioticus)
Explore G9VYV4 
Go to UniProtKB:  G9VYV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9VYV4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
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 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.23α = 90
b = 52.23β = 90
c = 214γ = 90
Software Package:
Software NamePurpose
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

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