Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 85.52 kDa 
• Atom Count: 6364 
• Modelled Residue Count: 774 
• Deposited Residue Count: 780 
• Unique protein chains: 1

5UC5

Chalcone synthase from Malus domestica

• PDB DOI: 10.2210/pdb5UC5/pdb

• Classification: TRANSFERASE
• Organism(s): Malus domestica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-21 Released: 2017-12-13 
• Deposition Author(s): Stewart Jr, C.E., Noel, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Molecular architectures of benzoic acid-specific type III polyketide synthases.

Stewart, C., Woods, K., Macias, G., Allan, A.C., Hellens, R.P., Noel, J.P.

(2017) Acta Crystallogr D Struct Biol 73: 1007-1019

• PubMed: 29199980 
• DOI: 10.1107/S2059798317016618
• Primary Citation of Related Structures:  
  5UC5, 5UCO, 5W8Q, 5WC4


• PubMed Abstract: 
  

Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica. Both biphenyl synthase and benzophenone synthase contain mutations that reshape their active-site cavities to prevent the binding of 4-coumaroyl-CoA and to favor the binding of small hydrophobic substrates. The active-site cavities of biphenyl synthase and benzophenone synthase also contain a novel pocket associated with their chain-elongation and cyclization reactions. Collectively, these results illuminate structural determinants of benzoic acid-specific type III PKSs and expand the understanding of the evolution of specialized metabolic pathways in plants.

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Organizational Affiliation: 

Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHS2 chalcone synthase	A, B	390	Malus domestica	Mutation(s): 0  EC: 2.3.1.74
UniProt
Find proteins for K9MUA0 (Malus domestica) Explore K9MUA0  Go to UniProtKB:  K9MUA0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.819	α = 90
b = 56.628	β = 90
c = 111.49	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL	data scaling
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-21 
• Released Date: 2017-12-13 
Deposition Author(s): Stewart Jr, C.E., Noel, J.P.

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release