PDBsum entry 1d6f

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protein ligands links
Transferase PDB id
Protein chain
389 a.a. *
Waters ×364
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Chalcone synthase c164a mutant
Structure: Chalcone synthase. Chain: a. Engineered: yes. Mutation: yes
Source: Medicago sativa. Organism_taxid: 3879. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.69Å     R-factor:   0.182     R-free:   0.201
Authors: J.M.Jez,J.L.Ferrer,M.E.Bowman,R.A.Dixon,J.P.Noel
Key ref:
J.M.Jez et al. (2000). Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase. Biochemistry, 39, 890-902. PubMed id: 10653632 DOI: 10.1021/bi991489f
13-Oct-99     Release date:   03-Feb-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P30074  (CHS2_MEDSA) -  Chalcone synthase 2
389 a.a.
389 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1021/bi991489f Biochemistry 39:890-902 (2000)
PubMed id: 10653632  
Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase.
J.M.Jez, J.L.Ferrer, M.E.Bowman, R.A.Dixon, J.P.Noel.
Chalcone synthase (CHS) catalyzes formation of the phenylpropanoid chalcone from one p-coumaroyl-CoA and three malonyl-coenzyme A (CoA) thioesters. The three-dimensional structure of CHS [Ferrer, J.-L., Jez, J. M., Bowman, M. E., Dixon, R. A., and Noel, J. P. (1999) Nat. Struct. Biol. 6, 775-784] suggests that four residues (Cys164, Phe215, His303, and Asn336) participate in the multiple decarboxylation and condensation reactions catalyzed by this enzyme. Here, we functionally characterize 16 point mutants of these residues for chalcone production, malonyl-CoA decarboxylation, and the ability to bind CoA and acetyl-CoA. Our results confirm Cys164's role as the active-site nucleophile in polyketide formation and elucidate the importance of His303 and Asn336 in the malonyl-CoA decarboxylation reaction. We suggest that Phe215 may help orient substrates at the active site during elongation of the polyketide intermediate. To better understand the structure-function relationships in some of these mutants, we also determined the crystal structures of the CHS C164A, H303Q, and N336A mutants refined to 1.69, 2.0, and 2.15 A resolution, respectively. The structure of the C164A mutant reveals that the proposed oxyanion hole formed by His303 and Asn336 remains undisturbed, allowing this mutant to catalyze malonyl-CoA decarboxylation without chalcone formation. The structures of the H303Q and N336A mutants support the importance of His303 and Asn336 in polarizing the thioester carbonyl of malonyl-CoA during the decarboxylation reaction. In addition, both of these residues may also participate in stabilizing the tetrahedral transition state during polyketide elongation. Conservation of the catalytic functions of the active-site residues may occur across a wide variety of condensing enzymes, including other polyketide and fatty acid synthases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22622584 M.N.Ngaki, G.V.Louie, R.N.Philippe, G.Manning, F.Pojer, M.E.Bowman, L.Li, E.Larsen, E.S.Wurtele, and J.P.Noel (2012).
Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis.
  Nature, 485, 530-533.
PDB codes: 4doi 4dok 4dol 4doo
  21448870 B.Boll, S.Hennig, C.Xie, J.K.Sohng, and L.Heide (2011).
Adenylate-forming enzymes of rubradirin biosynthesis: RubC1 is a bifunctional enzyme with aminocoumarin acyl ligase and tyrosine-activating domains.
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21439483 I.Höfer, M.Crüsemann, M.Radzom, B.Geers, D.Flachshaar, X.Cai, A.Zeeck, and J.Piel (2011).
Insights into the biosynthesis of hormaomycin, an exceptionally complex bacterial signaling metabolite.
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20055491 A.W.Schultz, C.A.Lewis, M.R.Luzung, P.S.Baran, and B.S.Moore (2010).
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20419468 C.Crocoll, J.Asbach, J.Novak, J.Gershenzon, and J.Degenhardt (2010).
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Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway.
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20419721 F.Lopez-Gallego, S.A.Agger, D.Abate-Pella, M.D.Distefano, and C.Schmidt-Dannert (2010).
Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers.
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20358127 I.Abe, and H.Morita (2010).
Structure and function of the chalcone synthase superfamily of plant type III polyketide synthases.
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20418426 L.Kaysser, E.Wemakor, S.Siebenberg, J.A.Salas, J.K.Sohng, B.Kammerer, and B.Gust (2010).
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Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens.
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Linking chemical and microbial diversity in marine sponges: possible role for poribacteria as producers of methyl-branched fatty acids.
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20937800 T.Kumano, T.Tomita, M.Nishiyama, and T.Kuzuyama (2010).
Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products.
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19996101 T.Okada, T.Tomita, A.P.Wulandari, T.Kuzuyama, and M.Nishiyama (2010).
Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus.
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PDB codes: 2ztj 2ztk 2zyf 3a9i
20467833 Y.J.Son, J.Y.Bae, S.H.Chong, H.S.Lee, S.H.Mo, T.Y.Kim, and H.Choe (2010).
Expression, high cell density culture and purification of recombinant EC-SOD in Escherichia coli.
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19694421 A.K.Bera, V.Atanasova, H.Robinson, E.Eisenstein, J.P.Coleman, E.C.Pesci, and J.F.Parsons (2009).
Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate.
  Biochemistry, 48, 8644-8655.
PDB codes: 3h76 3h77 3h78
19584923 A.L.Waite, P.Schaner, N.Richards, B.Balci-Peynircioglu, S.L.Masters, S.D.Brydges, M.Fox, A.Hong, E.Yilmaz, D.L.Kastner, E.L.Reinherz, and D.L.Gumucio (2009).
Pyrin Modulates the Intracellular Distribution of PSTPIP1.
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19379521 E.K.Bomati, G.Manning, and D.D.Deheyn (2009).
Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes.
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19739191 H.Deng, S.A.McMahon, A.S.Eustáquio, B.S.Moore, J.H.Naismith, and D.O'Hagan (2009).
Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62).
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PDB code: 2wr8
19581347 M.D.Marks, L.Tian, J.P.Wenger, S.N.Omburo, W.Soto-Fuentes, J.He, D.R.Gang, G.D.Weiblen, and R.A.Dixon (2009).
Identification of candidate genes affecting Delta9-tetrahydrocannabinol biosynthesis in Cannabis sativa.
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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.
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19605356 N.D.Adhikari, R.Orler, J.Chory, J.E.Froehlich, and R.M.Larkin (2009).
Porphyrins promote the association of GENOMES UNCOUPLED 4 and a Mg-chelatase subunit with chloroplast membranes.
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19400802 S.Agger, F.Lopez-Gallego, and C.Schmidt-Dannert (2009).
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus.
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19213732 S.Kumaran, H.Yi, H.B.Krishnan, and J.M.Jez (2009).
Assembly of the cysteine synthase complex and the regulatory role of protein-protein interactions.
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19635410 S.Y.Kim, P.Zhao, M.Igarashi, R.Sawa, T.Tomita, M.Nishiyama, and T.Kuzuyama (2009).
Cloning and heterologous expression of the cyclooctatin biosynthetic gene cluster afford a diterpene cyclase and two p450 hydroxylases.
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19557032 T.Ozaki, S.Mishima, M.Nishiyama, and T.Kuzuyama (2009).
NovQ is a prenyltransferase capable of catalyzing the addition of a dimethylallyl group to both phenylpropanoids and flavonoids.
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18059261 A.S.Eustáquio, F.Pojer, J.P.Noel, and B.S.Moore (2008).
Discovery and characterization of a marine bacterial SAM-dependent chlorinase.
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PDB codes: 2q6i 2q6k 2q6l 2q6o
18720493 A.S.Eustáquio, J.Härle, J.P.Noel, and B.S.Moore (2008).
S-Adenosyl-L-methionine hydrolase (adenosine-forming), a conserved bacterial and archaeal protein related to SAM-dependent halogenases.
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17924138 G.Arimura, S.Garms, M.Maffei, S.Bossi, B.Schulze, M.Leitner, A.Mithöfer, and W.Boland (2008).
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Zero erucic acid trait of rapeseed (Brassica napus L.) results from a deletion of four base pairs in the fatty acid elongase 1 gene.
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Engineering of plant polyketide biosynthesis.
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18476876 O.Yu, and J.M.Jez (2008).
Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides.
  Plant J, 54, 750-762.  
17912370 G.V.Louie, T.J.Baiga, M.E.Bowman, T.Koeduka, J.H.Taylor, S.M.Spassova, E.Pichersky, and J.P.Noel (2007).
Structure and reaction mechanism of basil eugenol synthase.
  PLoS ONE, 2, e993.
PDB codes: 2qw8 2qx7 2qys 2qzz 2r2g 2r6j
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Structural insight into chain-length control and product specificity of pentaketide chromone synthase from Aloe arborescens.
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PDB codes: 2d3m 2d51 2d52
17722151 J.Beekwilder, I.M.van der Meer, O.Sibbesen, M.Broekgaarden, I.Qvist, J.D.Mikkelsen, and R.D.Hall (2007).
Microbial production of natural raspberry ketone.
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A polyketide synthase of Plumbago indica that catalyzes the formation of hexaketide pyrones.
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17482864 K.Watanabe, A.P.Praseuth, and C.C.Wang (2007).
A comprehensive and engaging overview of the type III family of polyketide synthases.
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17240984 M.C.Moffitt, G.V.Louie, M.E.Bowman, J.Pence, J.P.Noel, and B.S.Moore (2007).
Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization.
  Biochemistry, 46, 1004-1012.
PDB codes: 2nyf 2nyn
17577899 N.Steffan, I.A.Unsöld, and S.M.Li (2007).
Chemoenzymatic synthesis of prenylated indole derivatives by using a 4-dimethylallyltryptophan synthase from Aspergillus fumigatus.
  Chembiochem, 8, 1298-1307.  
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.  
16245348 D.Xie, Z.Shao, J.Achkar, W.Zha, J.W.Frost, and H.Zhao (2006).
Microbial synthesis of triacetic acid lactone.
  Biotechnol Bioeng, 93, 727-736.  
17185228 G.V.Louie, M.E.Bowman, M.C.Moffitt, T.J.Baiga, B.S.Moore, and J.P.Noel (2006).
Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases.
  Chem Biol, 13, 1327-1338.
PDB codes: 2o6y 2o78 2o7b 2o7d 2o7e 2o7f
16339885 H.Singh, and R.H.Ashley (2006).
Redox regulation of CLIC1 by cysteine residues associated with the putative channel pore.
  Biophys J, 90, 1628-1638.  
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.  
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
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.  
15970585 E.K.Bomati, M.B.Austin, M.E.Bowman, R.A.Dixon, and J.P.Noel (2005).
Structural elucidation of chalcone reductase and implications for deoxychalcone biosynthesis.
  J Biol Chem, 280, 30496-30503.
PDB code: 1zgd
16166087 E.R.Bonner, R.E.Cahoon, S.M.Knapke, and J.M.Jez (2005).
Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana.
  J Biol Chem, 280, 38803-38813.
PDB codes: 1z7w 1z7y
15937191 L.Xiang, and B.S.Moore (2005).
Biochemical characterization of a prokaryotic phenylalanine ammonia lyase.
  J Bacteriol, 187, 4286-4289.  
15959519 T.Kuzuyama, J.P.Noel, and S.B.Richard (2005).
Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products.
  Nature, 435, 983-987.
PDB codes: 1zb6 1zcw 1zdw 1zdy
15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
  Annu Rev Plant Biol, 55, 85.  
15180996 J.M.Jez, R.E.Cahoon, and S.Chen (2004).
Arabidopsis thaliana glutamate-cysteine ligase: functional properties, kinetic mechanism, and regulation of activity.
  J Biol Chem, 279, 33463-33470.  
15302873 J.M.Jez, and R.E.Cahoon (2004).
Kinetic mechanism of glutathione synthetase from Arabidopsis thaliana.
  J Biol Chem, 279, 42726-42731.  
15265863 M.B.Austin, M.Izumikawa, M.E.Bowman, D.W.Udwary, J.L.Ferrer, B.S.Moore, and J.P.Noel (2004).
Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates.
  J Biol Chem, 279, 45162-45174.
PDB code: 1u0m
15353584 M.Weid, J.Ziegler, and T.M.Kutchan (2004).
The roles of latex and the vascular bundle in morphine biosynthesis in the opium poppy, Papaver somniferum.
  Proc Natl Acad Sci U S A, 101, 13957-13962.  
15604692 V.Hemleben, A.Dressel, B.Epping, R.Lukacin, S.Martens, and M.Austin (2004).
Characterization and structural features of a chalcone synthase mutation in a white-flowering line of Matthiola incana R. Br. (Brassicaceae).
  Plant Mol Biol, 55, 455-465.  
  12889743 C.D.Reeves (2003).
The enzymology of combinatorial biosynthesis.
  Crit Rev Biotechnol, 23, 95.  
12724310 I.Abe, Y.Sano, Y.Takahashi, and H.Noguchi (2003).
Site-directed mutagenesis of benzalacetone synthase. The role of the Phe215 in plant type III polyketide synthases.
  J Biol Chem, 278, 25218-25226.  
12866053 J.H.Dawe, C.T.Porter, J.M.Thornton, and A.B.Tabor (2003).
A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
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12594224 T.Brautaset, S.E.Borgos, H.Sletta, T.E.Ellingsen, and S.B.Zotchev (2003).
Site-specific mutagenesis and domain substitutions in the loading module of the nystatin polyketide synthase, and their effects on nystatin biosynthesis in Streptomyces noursei.
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11880657 A.Kodan, H.Kuroda, and F.Sakai (2002).
A stilbene synthase from Japanese red pine (Pinus densiflora): implications for phytoalexin accumulation and down-regulation of flavonoid biosynthesis.
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12354110 B.J.Blacklock, and J.G.Jaworski (2002).
Studies into factors contributing to substrate specificity of membrane-bound 3-ketoacyl-CoA synthases.
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12193782 H.J.Kwon, W.C.Smith, A.J.Scharon, S.H.Hwang, M.J.Kurth, and B.Shen (2002).
C-O bond formation by polyketide synthases.
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Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity.
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PDB code: 1jwx
11723138 N.Funa, Y.Ohnishi, Y.Ebizuka, and S.Horinouchi (2002).
Properties and substrate specificity of RppA, a chalcone synthase-related polyketide synthase in Streptomyces griseus.
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12086676 T.P.Roosild, S.Miller, I.R.Booth, and S.Choe (2002).
A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch.
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PDB codes: 1lss 1lsu
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Biosynthesis of polyketides in heterologous hosts.
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11828424 B.S.Moore, and J.N.Hopke (2001).
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11752437 H.Chen, C.C.Tseng, B.K.Hubbard, and C.T.Walsh (2001).
Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine.
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Benzalacetone synthase. A novel polyketide synthase that plays a crucial role in the biosynthesis of phenylbutanones in Rheum palmatum.
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11286890 J.G.Olsen, A.Kadziola, P.von Wettstein-Knowles, M.Siggaard-Andersen, and S.Larsen (2001).
Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery.
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PDB codes: 1ek4 1f91
11341960 M.Ghanevati, and J.G.Jaworski (2001).
Active-site residues of a plant membrane-bound fatty acid elongase beta-ketoacyl-CoA synthase, FAE1 KCS.
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  10888670 J.D.Leverson, C.A.Joazeiro, A.M.Page, H.Huang, P.Hieter, and T.Hunter (2000).
The APC11 RING-H2 finger mediates E2-dependent ubiquitination.
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11137815 J.M.Jez, M.B.Austin, J.Ferrer, M.E.Bowman, J.Schröder, and J.P.Noel (2000).
Structural control of polyketide formation in plant-specific polyketide synthases.
  Chem Biol, 7, 919-930.
PDB code: 1ee0
11054106 K.Springob, R.Lukacin, C.Ernwein, I.Gröning, and U.Matern (2000).
Specificities of functionally expressed chalcone and acridone synthases from Ruta graveolens.
  Eur J Biochem, 267, 6552-6559.  
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.