Biological Assembly 1  

 3D View: Structure | Electron Density

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: 84.97 kDa 
• Atom Count: 6253 
• Residue Count: 751 
• Unique protein chains: 1

3A5Q

Benzalacetone synthase from Rheum palmatum

• DOI: 10.2210/pdb3A5Q/pdb

• Classification: TRANSFERASE
• Organism(s): Rheum palmatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-10 Released: 2010-01-26 
• Deposition Author(s): Morita, H., Kato, R., Abe, I., Sugio, S., Kohno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.206 
• R-Value Work: 0.184 
• R-Value Observed: 0.189 

Literature

A structure-based mechanism for benzalacetone synthase from Rheum palmatum

Morita, H., Shimokawa, Y., Tanio, M., Kato, R., Noguchi, H., Sugio, S., Kohno, T., Abe, I.

(2010) Proc Natl Acad Sci U S A 107: 669-673

• PubMed: 20080733 
• DOI: 10.1073/pnas.0909982107
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Benzalacetone synthase (BAS), a plant-specific type III polyketide synthase (PKS), catalyzes a one-step decarboxylative condensation of malonyl-CoA and 4-coumaroyl-CoA to produce the diketide benzalacetone. We solved the crystal structures of both the wild-type and chalcone-producing I207L/L208F mutant of Rheum palmatum BAS at 1.8 A resolution. In addition, we solved the crystal structure of the wild-type enzyme, in which a monoketide coumarate intermediate is covalently bound to the catalytic cysteine residue, at 1.6 A resolution. This is the first direct evidence that type III PKS utilizes the cysteine as the nucleophile and as the attachment site for the polyketide intermediate. The crystal structures revealed that BAS utilizes an alternative, novel active-site pocket for locking the aromatic moiety of the coumarate, instead of the chalcone synthase's coumaroyl-binding pocket, which is lost in the active-site of the wild-type enzyme and restored in the I207L/L208F mutant. Furthermore, the crystal structures indicated the presence of a putative nucleophilic water molecule which forms hydrogen bond networks with the Cys-His-Asn catalytic triad. This suggested that BAS employs novel catalytic machinery for the thioester bond cleavage of the enzyme-bound diketide intermediate and the final decarboxylation reaction to produce benzalacetone. These findings provided a structural basis for the functional diversity of the type III PKS enzymes.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Benzalacetone synthase	A, B	387	Rheum palmatum	Mutation(s): 0  Gene Names: BAS EC: 2.3.1.212
Find proteins for Q94FV7 (Rheum palmatum) Explore Q94FV7  Go to UniProtKB:  Q94FV7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.206 
• R-Value Work: 0.184 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.635	α = 90
b = 89.612	β = 100.47
c = 81.068	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-10 
• Released Date: 2010-01-26 
Deposition Author(s): Morita, H., Kato, R., Abe, I., Sugio, S., Kohno, T.

Revision History 

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-06-27
  Changes: Database references