3SLK

Structure of ketoreductase and enoylreductase didomain from modular polyketide synthase

• PDB DOI: https://doi.org/10.2210/pdb3SLK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharopolyspora spinosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-24 Released: 2012-05-30 
• Deposition Author(s): Zheng, J., Gay, D.C., Keatinge-Clay, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Divergence of multimodular polyketide synthases revealed by a didomain structure.

Zheng, J., Gay, D.C., Demeler, B., White, M.A., Keatinge-Clay, A.T.

(2012) Nat Chem Biol 8: 615-621

• PubMed: 22634636 
• DOI: https://doi.org/10.1038/nchembio.964
• Primary Citation of Related Structures:  
  3SLK


• PubMed Abstract: 
  

  The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 170.12 kDa 
• Atom Count: 11,217 
• Modelled Residue Count: 1,494 
• Deposited Residue Count: 1,590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase extender module 2	A, B	795	Saccharopolyspora spinosa	Mutation(s): 0  Gene Names: spnB EC: 1.1.1.100 (PDB Primary Data), 1.3.1.9 (PDB Primary Data)
UniProt
Find proteins for Q9ALM5 (Saccharopolyspora spinosa) Explore Q9ALM5  Go to UniProtKB:  Q9ALM5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth A], G [auth B], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SO4	E [auth A], F [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.256 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.104	α = 90
b = 110.195	β = 90
c = 202.857	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Zheng, J., Gay, D.C., Keatinge-Clay, A.T.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Database references
• Version 1.2: 2012-09-05
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations