5W8Q

Crystal structure of biphenyl synthase from Malus domestica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.173 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.098 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1107/S2059798317016618
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIS3 biphenyl synthase
A, B
390Malus domesticaMutation(s): 0 
EC: 2.3.1.177
Find proteins for K9MST3 (Malus domestica)
Go to UniProtKB:  K9MST3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU4
Query on BU4

Download SDF File 
Download CCD File 
A, B
(3R)-butane-1,3-diol
C4 H10 O2
PUPZLCDOIYMWBV-SCSAIBSYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.173 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.098 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.270α = 90.00
b = 113.020β = 93.15
c = 62.770γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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