5YDM

The crystal structure of the Acyl Transferase domain of SpnD complex with benzylmalonyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin.

Li, Y.Zhang, W.Zhang, H.Tian, W.Y.Wu, L.Wang, S.W.Zheng, M.M.Zhang, J.R.Sun, C.H.Deng, Z.X.Sun, Y.H.Qu, X.D.Zhou, J.H.

(2018) Angew Chem Int Ed Engl 57: 5823-5827

  • DOI: 10.1002/anie.201802805
  • Primary Citation of Related Structures:  
    5YDA, 5YDL, 5YDM

  • PubMed Abstract: 
  • Polyketides are a large family of pharmaceutically important natural products, and the structural modification of their scaffolds is significant for drug development. Herein, we report high-resolution X-ray crystal structures of the broadly selective acyltransferase (AT) from the splenocin polyketide synthase (SpnD-AT) in the apo form and in complex with benzylmalonyl and pentynylmalonyl extender unit mimics ...

    Polyketides are a large family of pharmaceutically important natural products, and the structural modification of their scaffolds is significant for drug development. Herein, we report high-resolution X-ray crystal structures of the broadly selective acyltransferase (AT) from the splenocin polyketide synthase (SpnD-AT) in the apo form and in complex with benzylmalonyl and pentynylmalonyl extender unit mimics. These structures revealed the molecular basis for the stereoselectivity and substrate specificity of SpnD-AT, and enabled the engineering of the industrially important Ery-AT6 to broaden its substrate scope to include three new types of extender units.


    Organizational Affiliation

    Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PKSA433Streptomyces sp. CNQ431Mutation(s): 0 
Gene Names: spnD
UniProt
Find proteins for A0A0E3JLZ0 (Streptomyces sp. CNQ431)
Explore A0A0E3JLZ0 
Go to UniProtKB:  A0A0E3JLZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3JLZ0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUW
Query on DUW

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-methanoyl-3-phenyl-propanoic acid
C10 H10 O3
NAYOGLQOGCMXAU-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.927α = 90
b = 108.927β = 90
c = 144.838γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data 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: 2018-05-23
    Type: Initial release