4J1Q | pdb_00004j1q

Crystal structure of a ketoreductase domain from the bacillaene assembly line


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective alpha- and beta-ketoreduction.

Piasecki, S.K.Zheng, J.Axelrod, A.J.E Detelich, M.Keatinge-Clay, A.T.

(2014) Proteins 82: 2067-2077

  • DOI: https://doi.org/10.1002/prot.24561
  • Primary Citation Related Structures: 
    4J1Q, 4J1S

  • PubMed Abstract: 

    While the cis-acyltransferase modular polyketide synthase assembly lines have largely been structurally dissected, enzymes from within the recently discovered trans-acyltransferase polyketide synthase assembly lines are just starting to be observed crystallographically. Here we examine the ketoreductase (KR) from the first polyketide synthase module of the bacillaene nonribosomal peptide synthetase/polyketide synthase at 2.35-Å resolution. This KR naturally reduces both α- and β-keto groups and is the only KR known to do so during the biosynthesis of a polyketide. The isolated KR not only reduced an N-acetylcysteamine-bound β-keto substrate to a D-β-hydroxy product, but also an N-acetylcysteamine-bound α-keto substrate to an L-α-hydroxy product. That the substrates must enter the active site from opposite directions to generate these stereochemistries suggests that the acyl-phosphopantetheine moiety is capable of accessing very different conformations despite being anchored to a serine residue of a docked acyl carrier protein. The features enabling stereocontrolled α-ketoreduction may not be extensive since a KR that naturally reduces a β-keto group within a cis-acyltransferase polyketide synthase was identified that performs a completely stereoselective reduction of the same α-keto substrate to generate the D-α-hydroxy product. A sequence analysis of trans-acyltransferase KRs reveals that a single residue, rather than a three-residue motif found in cis-acyltransferase KRs, is predictive of the orientation of the resulting β-hydroxyl group.


  • Organizational Affiliation
    • Institute for Cellular and Molecular Biology, The University of Texas at Austin, Texas, 78712.

Macromolecule Content 

  • Total Structure Weight: 53.26 kDa 
  • Atom Count: 3,378 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyketide synthase PksJ464Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU17180pksJpksJ (amino acids 2669-3111)pksK
EC: 1.1.1.100
UniProt
Find proteins for P40806 (Bacillus subtilis (strain 168))
Explore P40806 
Go to UniProtKB:  P40806
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40806
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.529α = 90
b = 59.529β = 90
c = 220.792γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Database references
  • Version 1.3: 2014-09-03
    Changes: Database references
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations