The crystal structure of the Acyl Transferase domain of SpnD

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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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: https://doi.org/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. 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

    Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PKS433Streptomyces sp. CNQ431Mutation(s): 0 
Gene Names: spnD
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
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.78α = 90
b = 109.78β = 90
c = 142.573γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references