PDBsum entry 1u0w

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Transferase PDB id
Protein chains
388 a.a. *
STL ×4
Waters ×1190
* Residue conservation analysis
PDB id:
Name: Transferase
Title: An aldol switch discovered in stilbene synthases mediates cyclization specificity of type iii polyketide synthases: 18xchs+resveratrol structure
Structure: Chalcone synthase 2. Chain: a, b, c, d. Synonym: naringenin-chalcone synthase 2. Engineered: yes. Mutation: yes
Source: Medicago sativa. Organism_taxid: 3879. Gene: chs2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.203     R-free:   0.264
Authors: M.B.Austin,M.E.Bowman,J.-L.Ferrer,J.Schroder,J.P.Noel
Key ref:
M.B.Austin et al. (2004). An aldol switch discovered in stilbene synthases mediates cyclization specificity of type III polyketide synthases. Chem Biol, 11, 1179-1194. PubMed id: 15380179 DOI: 10.1016/j.chembiol.2004.05.024
14-Jul-04     Release date:   12-Oct-04    
Go to PROCHECK summary

Protein chains
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 18 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
Bound ligand (Het Group name = STL)
matches with 85.00% similarity
+ 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: 10.1016/j.chembiol.2004.05.024 Chem Biol 11:1179-1194 (2004)
PubMed id: 15380179  
An aldol switch discovered in stilbene synthases mediates cyclization specificity of type III polyketide synthases.
M.B.Austin, M.E.Bowman, J.L.Ferrer, J.Schröder, J.P.Noel.
Stilbene synthase (STS) and chalcone synthase (CHS) each catalyze the formation of a tetraketide intermediate from a CoA-tethered phenylpropanoid starter and three molecules of malonyl-CoA, but use different cyclization mechanisms to produce distinct chemical scaffolds for a variety of plant natural products. Here we present the first STS crystal structure and identify, by mutagenic conversion of alfalfa CHS into a functional stilbene synthase, the structural basis for the evolution of STS cyclization specificity in type III polyketide synthase (PKS) enzymes. Additional mutagenesis and enzymatic characterization confirms that electronic effects rather than steric factors balance competing cyclization specificities in CHS and STS. Finally, we discuss the problematic in vitro reconstitution of plant stilbenecarboxylate pathways, using insights from existing biomimetic polyketide cyclization studies to generate a novel mechanistic hypothesis to explain stilbenecarboxylate biosynthesis.
  Selected figure(s)  
Figure 3.
Figure 3. Thioesterase-like STS “Aldol Switch” Controls Cyclization Specificity(A) Slightly different bound conformations of resveratrol observed in the complexed 18xCHS crystal structure (green and rose) correlate to movements of the flexible Phe265 side chain, overlaid with the structure of the previously determined resveratrol [12] bound in wild-type CHS (light gray) and viewed down the CoA binding tunnel into the active site cavity. Positioning of resveratrol's starter- and malonyl-derived aromatic rings are similar to each other and to CHS-bound naringenin (shown in Figure 1B in a similar view).(B) C-α trace overlay of the displacement of the area 2 loop in STS (gold) and 18xCHS (green), compared to CHS (blue). Two orientations illustrate the positions and movements of residues 131–133 (CHS numbering).(C) Stereoview of the 18xCHS STS-like “aldol switch” hydrogen bonds, showing the 1.9 Å resolution 2F[o] − F[c] electron density map (blue wirecage) contoured at 1 sigma.(D) “Aldol switch” hydrogen bonding differences (resulting from repositioning of the Thr132 side chain) in CHS-like and STS-like active sites, compared to each other and to the active site of thioesterase II (TEII) from E. coli ([18]; PDB code 1C8U). Distances incompatible with hydrogen bond formation are given in parentheses and indicated with double-headed arrows. Putative nucleophilic water positions are highlighted in yellow.(E) Thin layer chromatography (TLC) analysis of the cyclization specificities of mutants designed to disrupt the 18xCHS mutant's aldol switch hydrogen bond network while preserving the 18xCHS STS-like conformational changes (see text).
Figure 4.
Figure 4. STS Mechanistic Options and Relevant Solution Chemistry(A) Spontaneous solution-based polyketide C2→C7 aldol condensation cyclization chemistry leading to stilbenes. Atoms fated for elimination as molecules of CO[2] and H[2]O are colored in red and blue, respectively. The aromatized stilbene acid solution-based intermediate product has been shown not to be an intermediate in the STS-catalyzed reaction (see text).(B) Plausible reaction pathways for the four STS cyclization-related events, assuming mechanistic divergence from CHS begins with an aldol switch-catalyzed thioesterase-like hydrolytic step. Scenario One depicts a decarboxylative cyclization reaction, as described by Ebizuka's group [14]. Scenario Two depicts two alternative decarboxylation schemes that follow a solution chemistry-like nondecarboxylative aldol condensation-based cyclization. Atoms fated for elimination as molecules of CO[2] and H[2]O are again colored red and blue, respectively.
  The above figures are reprinted by permission from Cell Press: Chem Biol (2004, 11, 1179-1194) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21117241 K.Miyazono, J.Um, F.L.Imai, Y.Katsuyama, Y.Ohnishi, S.Horinouchi, and M.Tanokura (2011).
Crystal structure of curcuminoid synthase CUS from Oryza sativa.
  Proteins, 79, 669-673.
PDB code: 3oit
20348430 D.Cook, A.M.Rimando, T.E.Clemente, J.Schröder, F.E.Dayan, N.P.Nanayakkara, Z.Pan, B.P.Noonan, M.Fishbein, I.Abe, S.O.Duke, and S.R.Baerson (2010).
Alkylresorcinol synthases expressed in Sorghum bicolor root hairs play an essential role in the biosynthesis of the allelopathic benzoquinone sorgoleone.
  Plant Cell, 22, 867-887.  
21041675 H.Morita, K.Wanibuchi, H.Nii, R.Kato, S.Sugio, and I.Abe (2010).
Structural basis for the one-pot formation of the diarylheptanoid scaffold by curcuminoid synthase from Oryza sativa.
  Proc Natl Acad Sci U S A, 107, 19778-19783.
PDB code: 3ale
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.  
  20726013 P.Jeandet, B.Delaunois, A.Conreux, D.Donnez, V.Nuzzo, S.Cordelier, C.Clément, and E.Courot (2010).
Biosynthesis, metabolism, molecular engineering, and biological functions of stilbene phytoalexins in plants.
  Biofactors, 36, 331-341.  
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.  
20853106 X.Gao, P.Wang, and Y.Tang (2010).
Engineered polyketide biosynthesis and biocatalysis in Escherichia coli.
  Appl Microbiol Biotechnol, 88, 1233-1242.  
19116720 J.Condori, G.Medrano, G.Sivakumar, V.Nair, C.Cramer, and F.Medina-Bolivar (2009).
Functional characterization of a stilbene synthase gene using a transient expression system in planta.
  Plant Cell Rep, 28, 589-599.  
19443619 K.Hanhineva, H.Kokko, H.Siljanen, I.Rogachev, A.Aharoni, and S.O.Kärenlampi (2009).
Stilbene synthase gene transfer caused alterations in the phenylpropanoid metabolism of transgenic strawberry (Fragariaxananassa).
  J Exp Bot, 60, 2093-2106.  
19507202 M.Tosin, D.Spiteller, and J.B.Spencer (2009).
Malonyl carba(dethia)- and malonyl oxa(dethia)-coenzyme A as tools for trapping polyketide intermediates.
  Chembiochem, 10, 1714-1723.  
19432534 S.Pervaiz, and A.L.Holme (2009).
Resveratrol: its biologic targets and functional activity.
  Antioxid Redox Signal, 11, 2851-2897.  
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.  
19266535 T.L.Li, D.Spiteller, and J.B.Spencer (2009).
Identification of a pentaketide stilbene produced by a type III polyketide synthase from Pinus sylvestris and characterisation of free coenzyme A intermediates.
  Chembiochem, 10, 896-901.  
19348024 Y.Mizuuchi, S.P.Shi, K.Wanibuchi, A.Kojima, H.Morita, H.Noguchi, and I.Abe (2009).
Novel type III polyketide synthases from Aloe arborescens.
  FEBS J, 276, 2391-2401.  
18191264 C.Halls, and O.Yu (2008).
Potential for metabolic engineering of resveratrol biosynthesis.
  Trends Biotechnol, 26, 77-81.  
  18323613 C.Taguchi, F.Taura, T.Tamada, Y.Shoyama, Y.Shoyama, H.Tanaka, R.Kuroki, and S.Morimoto (2008).
Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 217-220.  
  18391433 H.Morita, M.Tanio, S.Kondo, R.Kato, K.Wanibuchi, H.Noguchi, S.Sugio, I.Abe, and T.Kohno (2008).
Crystallization and preliminary crystallographic analysis of a plant type III polyketide synthase that produces benzalacetone.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 304-306.  
18981598 I.Abe (2008).
Engineering of plant polyketide biosynthesis.
  Chem Pharm Bull (Tokyo), 56, 1505-1514.  
18347585 M.B.Austin, P.E.O'Maille, and J.P.Noel (2008).
Evolving biosynthetic tangos negotiate mechanistic landscapes.
  Nat Chem Biol, 4, 217-222.  
18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
  Plant J, 54, 750-762.  
18940668 S.B.Rubin-Pitel, H.Zhang, T.Vu, J.S.Brunzelle, H.Zhao, and S.K.Nair (2008).
Distinct structural elements dictate the specificity of the type III pentaketide synthase from Neurospora crassa.
  Chem Biol, 15, 1079-1090.
PDB codes: 3euo 3euq 3eut
19043200 Y.Mizuuchi, Y.Shimokawa, K.Wanibuchi, H.Noguchi, and I.Abe (2008).
Structure function analysis of novel type III polyketide synthases from Arabidopsis thaliana.
  Biol Pharm Bull, 31, 2205-2210.  
17109150 B.Liu, T.Raeth, T.Beuerle, and L.Beerhues (2007).
Biphenyl synthase, a novel type III polyketide synthase.
  Planta, 225, 1495-1503.  
  17620714 H.Morita, S.Kondo, R.Kato, K.Wanibuchi, H.Noguchi, S.Sugio, I.Abe, and T.Kohno (2007).
Crystallization and preliminary crystallographic analysis of an acridone-producing novel multifunctional type III polyketide synthase from Huperzia serrata.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 576-578.  
17462571 H.Morita, S.Kondo, S.Oguro, H.Noguchi, S.Sugio, I.Abe, and T.Kohno (2007).
Structural insight into chain-length control and product specificity of pentaketide chromone synthase from Aloe arborescens.
  Chem Biol, 14, 359-369.
PDB codes: 2d3m 2d51 2d52
17698806 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.
  Proc Natl Acad Sci U S A, 104, 13632-13637.
PDB codes: 2jiz 2jj1 2jj2
17229146 K.Springob, S.Samappito, A.Jindaprasert, J.Schmidt, J.E.Page, W.De-Eknamkul, and T.M.Kutchan (2007).
A polyketide synthase of Plumbago indica that catalyzes the formation of hexaketide pyrones.
  FEBS J, 274, 406-417.  
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.  
17374612 N.Funa, T.Awakawa, and S.Horinouchi (2007).
Pentaketide resorcylic acid synthesis by type III polyketide synthase from Neurospora crassa.
  J Biol Chem, 282, 14476-14481.  
17932040 Y.Katsuyama, M.Matsuzawa, N.Funa, and S.Horinouchi (2007).
In vitro synthesis of curcuminoids by type III polyketide synthase from Oryza sativa.
  J Biol Chem, 282, 37702-37709.  
16356722 A.M.Haapalainen, G.Meriläinen, and R.K.Wierenga (2006).
The thiolase superfamily: condensing enzymes with diverse reaction specificities.
  Trends Biochem Sci, 31, 64-71.  
16785438 B.T.Greenhagen, P.E.O'Maille, J.P.Noel, and J.Chappell (2006).
Identifying and manipulating structural determinates linking catalytic specificities in terpene synthases.
  Proc Natl Acad Sci U S A, 103, 9826-9831.  
16864776 F.Pojer, J.L.Ferrer, S.B.Richard, D.A.Nagegowda, M.L.Chye, T.J.Bach, and J.P.Noel (2006).
Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases.
  Proc Natl Acad Sci U S A, 103, 11491-11496.
PDB codes: 2f82 2f9a 2fa0 2fa3
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.  
16906151 M.B.Austin, T.Saito, M.E.Bowman, S.Haydock, A.Kato, B.S.Moore, R.R.Kay, and J.P.Noel (2006).
Biosynthesis of Dictyostelium discoideum differentiation-inducing factor by a hybrid type I fatty acid-type III polyketide synthase.
  Nat Chem Biol, 2, 494-502.
PDB code: 2h84
17086177 M.S.Donia, B.J.Hathaway, S.Sudek, M.G.Haygood, M.J.Rosovitz, J.Ravel, and E.W.Schmidt (2006).
Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians.
  Nat Chem Biol, 2, 729-735.  
16597676 N.Funa, H.Ozawa, A.Hirata, and S.Horinouchi (2006).
Phenolic lipid synthesis by type III polyketide synthases is essential for cyst formation in Azotobacter vinelandii.
  Proc Natl Acad Sci U S A, 103, 6356-6361.  
16611080 N.Labinskyy, A.Csiszar, G.Veress, G.Stef, P.Pacher, G.Oroszi, J.Wu, and Z.Ungvari (2006).
Vascular dysfunction in aging: potential effects of resveratrol, an anti-inflammatory phytoestrogen.
  Curr Med Chem, 13, 989-996.  
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.  
16931521 W.Zha, S.B.Rubin-Pitel, and H.Zhao (2006).
Characterization of the substrate specificity of PhlD, a type III polyketide synthase from Pseudomonas fluorescens.
  J Biol Chem, 281, 32036-32047.  
15860421 J.P.Noel, M.B.Austin, and E.K.Bomati (2005).
Structure-function relationships in plant phenylpropanoid biosynthesis.
  Curr Opin Plant Biol, 8, 249-253.  
16028220 Y.Shomura, I.Torayama, D.Y.Suh, T.Xiang, A.Kita, U.Sankawa, and K.Miki (2005).
Crystal structure of stilbene synthase from Arachis hypogaea.
  Proteins, 60, 803-806.
PDB codes: 1z1e 1z1f
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