5YDL | pdb_00005ydl

The crystal structure of the Acyl Transferase domain of SpnD complex with 2-(pent-4-yn-1-yl)malonyl

• PDB DOI: https://doi.org/10.2210/pdb5YDL/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces sp. CNQ431
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-09-13 Released: 2018-05-23 
• Deposition Author(s): Li, Y., Qu, X.D., Zhou, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

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

• PubMed: 29536601 
• 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.

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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.
State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.4 kDa 
• Atom Count: 3,204 
• Modeled Residue Count: 408 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PKS	A	433	Streptomyces sp. CNQ431	Mutation(s): 0  Gene Names: spnD
UniProt
Find proteins for A0A0E3JLZ0 (Streptomyces sp. CNQ431) Explore A0A0E3JLZ0  Go to UniProtKB:  A0A0E3JLZ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUV	B [auth A]	(2R)-2-methanoylhept-6-ynoic acid C8 H10 O3 XEBGKYCHRCIWRY-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.02	α = 90
b = 109.02	β = 90
c = 144.289	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Li, Y., Qu, X.D., Zhou, J.H.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary