PDBsum entry 1jwx

Go to PDB code: 
protein links
Transferase PDB id
Jmol PyMol
Protein chain
388 a.a. *
Waters ×344
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Chalcone synthase--f215s mutant
Structure: Chalcone synthase 2. Chain: a. Synonym: naringenin-chalcone synthase 2. Engineered: yes. Mutation: yes
Source: Medicago sativa. Organism_taxid: 3879. Gene: chs2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
1.63Å     R-factor:   0.200     R-free:   0.225
Authors: J.M.Jez,M.E.Bowman,J.P.Noel
Key ref:
J.M.Jez et al. (2002). Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity. Proc Natl Acad Sci U S A, 99, 5319-5324. PubMed id: 11959984 DOI: 10.1073/pnas.082590499
05-Sep-01     Release date:   24-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P30074  (CHS2_MEDSA) -  Chalcone synthase 2
389 a.a.
388 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Naringenin-chalcone synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Chalcone and Stilbene Biosynthesis
      Reaction: 3 malonyl-CoA + 4-coumaroyl-CoA = 4 CoA + naringenin chalcone + 3 CO2
3 × malonyl-CoA
+ 4-coumaroyl-CoA
= 4 × CoA
+ naringenin chalcone
+ 3 × CO(2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1073/pnas.082590499 Proc Natl Acad Sci U S A 99:5319-5324 (2002)
PubMed id: 11959984  
Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity.
J.M.Jez, M.E.Bowman, J.P.Noel.
Type III polyketide synthases (PKS) generate an array of natural products by condensing multiple acetyl units derived from malonyl-CoA to thioester-linked starter molecules covalently bound in the PKS active site. One strategy adopted by Nature for increasing the functional diversity of these biosynthetic enzymes involves modifying polyketide assembly by altering the preference for starter molecules. Chalcone synthase (CHS) is a ubiquitous plant PKS and the first type III PKS described functionally and structurally. Guided by the three-dimensional structure of CHS, Phe-215 and Phe-265, which are situated at the active site entrance, were targeted for site-directed mutagenesis to diversify CHS activity. The resulting mutants were screened against a panel of aliphatic and aromatic CoA-linked starter molecules to evaluate the degree of starter molecule specificity in CHS. Although wild-type CHS accepts a number of natural CoA thioesters, it does not use N-methylanthraniloyl-CoA as a substrate. Substitution of Phe-215 by serine yields a CHS mutant that preferentially accepts this CoA-thioester substrate to generate a novel alkaloid, namely N-methylanthraniloyltriacetic acid lactone. These results demonstrate that a point mutation in CHS dramatically shifts the molecular selectivity of this enzyme. This structure-based approach to metabolic redesign represents an initial step toward tailoring the biosynthetic activity of plant type III PKS.
  Selected figure(s)  
Figure 1.
Fig. 1. Overview of plant type III polyketide synthases. (A) Reactions catalyzed by CHS and ACS. Only the starter molecules are shown. Both enzymes use three molecules of malonyl-CoA during the elongation of the starter molecule. Chalcone is on top and acridone is on the bottom. (B) Ribbon diagram of the CHS homodimer showing the catalytic residues (Cys-164, His-303, and Asn-336) and the two phenylalanines (Phe-215 and Phe-265) at the boundary between the CoA (gold) binding site and the active site of one monomer. Figure prepared with MOLSCRIPT (35) and POV-RAY [POV-Team (1997) POV-RAY, Persistence of Vision Ray-Tracer;].
Figure 4.
Fig. 4. Structure of the F215S mutant active site and model of starter molecule binding. (A) Stereo-view illustrates the active site of the F215S mutant, including the catalytic residues (Cys-164, His-303, and Asn-336) and Phe-265. Both conformers of Ser-215 are shown. The CoA-thioester extends from the left side of the view. N-methylanthraniloyl-CoA has been modeled by applying the structural restraints discussed in the text. (B) Stereo-view of the wild-type CHS active site with N-methylanthraniloyl-CoA modeled at the entrance. Steric clashes with Phe-215 prevent the CoA-thioester from adopting the conformation depicted in A. (C) Stereo-view of the wild-type CHS active site with p-coumaroyl-CoA modeled at the entrance highlighting the ability of the propanoid moiety to extend the phenolic ring deep into the active site.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080733 H.Morita, Y.Shimokawa, M.Tanio, R.Kato, H.Noguchi, S.Sugio, T.Kohno, and I.Abe (2010).
A structure-based mechanism for benzalacetone synthase from Rheum palmatum.
  Proc Natl Acad Sci U S A, 107, 669-673.
PDB codes: 3a5q 3a5r 3a5s
20358127 I.Abe, and H.Morita (2010).
Structure and function of the chalcone synthase superfamily of plant type III polyketide synthases.
  Nat Prod Rep, 27, 809-838.  
19876746 P.K.Koduri, G.S.Gordon, E.I.Barker, C.C.Colpitts, N.W.Ashton, and D.Y.Suh (2010).
Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens.
  Plant Mol Biol, 72, 247-263.  
19710020 T.Klundt, M.Bocola, M.Lütge, T.Beuerle, B.Liu, and L.Beerhues (2009).
A single amino acid substitution converts benzophenone synthase into phenylpyrone synthase.
  J Biol Chem, 284, 30957-30964.  
18476861 B.J.Nikolau, M.A.Perera, L.Brachova, and B.Shanks (2008).
Platform biochemicals for a biorenewable chemical industry.
  Plant J, 54, 536-545.  
18191264 C.Halls, and O.Yu (2008).
Potential for metabolic engineering of resveratrol biosynthesis.
  Trends Biotechnol, 26, 77-81.  
18981598 I.Abe (2008).
Engineering of plant polyketide biosynthesis.
  Chem Pharm Bull (Tokyo), 56, 1505-1514.  
18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
  Plant J, 54, 750-762.  
17250741 K.Wanibuchi, P.Zhang, T.Abe, H.Morita, T.Kohno, G.Chen, H.Noguchi, and I.Abe (2007).
An acridone-producing novel multifunctional type III polyketide synthase from Huperzia serrata.
  FEBS J, 274, 1073-1082.  
17482864 K.Watanabe, A.P.Praseuth, and C.C.Wang (2007).
A comprehensive and engaging overview of the type III family of polyketide synthases.
  Curr Opin Chem Biol, 11, 279-286.  
17217457 T.Sinlapadech, J.Stout, M.O.Ruegger, M.Deak, and C.Chapple (2007).
The hyper-fluorescent trichome phenotype of the brt1 mutant of Arabidopsis is the result of a defect in a sinapic acid: UDPG glucosyltransferase.
  Plant J, 49, 655-668.  
16575575 C.D.Dana, D.R.Bevan, and B.S.Winkel (2006).
Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure.
  J Mol Model, 12, 905-914.  
16367761 I.Abe, T.Watanabe, W.Lou, and H.Noguchi (2006).
Active site residues governing substrate selectivity and polyketide chain length in aloesone synthase.
  FEBS J, 273, 208-218.  
16551366 K.T.Watts, P.C.Lee, and C.Schmidt-Dannert (2006).
Biosynthesis of plant-specific stilbene polyketides in metabolically engineered Escherichia coli.
  BMC Biotechnol, 6, 22.  
16496097 S.Brand, D.Hölscher, A.Schierhorn, A.Svatos, J.Schröder, and B.Schneider (2006).
A type III polyketide synthase from Wachendorfia thyrsiflora and its role in diarylheptanoid and phenylphenalenone biosynthesis.
  Planta, 224, 413-428.  
15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
  Annu Rev Plant Biol, 55, 85.  
12795704 B.Liu, H.Falkenstein-Paul, W.Schmidt, and L.Beerhues (2003).
Benzophenone synthase and chalcone synthase from Hypericum androsaemum cell cultures: cDNA cloning, functional expression, and site-directed mutagenesis of two polyketide synthases.
  Plant J, 34, 847-855.  
  12889743 C.D.Reeves (2003).
The enzymology of combinatorial biosynthesis.
  Crit Rev Biotechnol, 23, 95.  
12631695 C.R.Hutchinson (2003).
Polyketide and non-ribosomal peptide synthases: falling together by coming apart.
  Proc Natl Acad Sci U S A, 100, 3010-3012.  
12470730 N.L.Pohl (2002).
Nonnatural substrates for polyketide synthases and their associated modifying enzymes.
  Curr Opin Chem Biol, 6, 773-778.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.