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PDBsum entry 2d3m

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2d3m
Jmol
Contents
Protein chains
405 a.a. *
Ligands
COA ×2
Waters ×566
* Residue conservation analysis
PDB id:
2d3m
Name: Transferase
Title: Pentaketide chromone synthase complexed with coenzyme a
Structure: Pentaketide chromone synthase. Chain: a, b. Engineered: yes
Source: Aloe arborescens. Organism_taxid: 45385. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.198     R-free:   0.207
Authors: H.Morita,S.Kondo,S.Oguro,H.Noguchi,S.Sugio,I.Abe,T.Kohno
Key ref:
H.Morita et al. (2007). Structural insight into chain-length control and product specificity of pentaketide chromone synthase from Aloe arborescens. Chem Biol, 14, 359-369. PubMed id: 17462571 DOI: 10.1016/j.chembiol.2007.02.003
Date:
29-Sep-05     Release date:   24-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58VP7  (Q58VP7_ALOAR) -  5,7-dihydroxy-2-methylchromone synthase
Seq:
Struc:
403 a.a.
405 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.2.3.1.216  - 5,7-dihydroxy-2-methylchromone synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5 malonyl-CoA = 5 CoA + 5,7-dihydroxy-2-methyl-4H-chromen-4-one + 5 CO2 + H2O
5 × malonyl-CoA
= 5 × CoA
+ 5,7-dihydroxy-2-methyl-4H-chromen-4-one
+ 5 × CO(2)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.chembiol.2007.02.003 Chem Biol 14:359-369 (2007)
PubMed id: 17462571  
 
 
Structural insight into chain-length control and product specificity of pentaketide chromone synthase from Aloe arborescens.
H.Morita, S.Kondo, S.Oguro, H.Noguchi, S.Sugio, I.Abe, T.Kohno.
 
  ABSTRACT  
 
The crystal structures of a wild-type and a mutant PCS, a novel plant type III polyketide synthase from a medicinal plant, Aloe arborescens, were solved at 1.6 A resolution. The crystal structures revealed that the pentaketide-producing wild-type and the octaketide-producing M207G mutant shared almost the same overall folding, and that the large-to-small substitution dramatically increases the volume of the polyketide-elongation tunnel by opening a gate to two hidden pockets behind the active site of the enzyme. The chemically inert active site residue 207 thus controls the number of condensations of malonyl-CoA, solely depending on the steric bulk of the side chain. These findings not only provided insight into the polyketide formation reaction, but they also suggested strategies for the engineered biosynthesis of polyketides.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overall Structure of PCS Complexed with CoA-SH
(A) Ribbon representation of the PCS homodimer. The monomers are colored green and silver, and the CoA-SH molecules are shown as blue stick models. The catalytic Cys174 and Met147, which form a partial wall of the active-site cavity of another monomer, are highlighted as yellow CPK and stick models, respectively.
(B) Comparison of PCS (green), M. sativa CHS (blue), and G. hybrida 2PS (purple). The catalytic Cys174 and the bound CoA-SH in PCS are also shown as yellow and red CPK molecules, respectively.
(C) CoA-SH binding to the PCS structure. The CoA-SH (green) and the SIGMA-weighted |2F[o] − F[c]| electron density (0.8σ, red cage) for CoA-SH are shown. The water molecules (light-blue spheres) and hydrogen bonds (dotted lines) are also indicated.
Figure 6.
Figure 6. Schematic Representation of the Active-Site Architecture of Wild-Type PCS, the M207G Mutant, and M. sativa CHS
(A–C) The M207G substitution opens a gate to the buried pocket A that extends into the “floor” of the active-site cavity, resulting in a 4:1 mixture of SEK4b:SEK4 instead of 5,7-dihydroxy- 2-methylchormone. PCS locks the methyl end of its linear pentaketide intermediate between Met207 and Val351, as in the case in which M. sativa CHS locks the aromatic ring derived from 4-coumaroyl-CoA with the coumaroyl-binding pocket.
 
  The above figures are reprinted by permission from Cell Press: Chem Biol (2007, 14, 359-369) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
19177221 I.Fujii (2009).
Heterologous expression systems for polyketide synthases.
  Nat Prod Rep, 26, 155-169.  
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.  
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.  
  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.  
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.  
  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.  
  18007047 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 octaketide-producing plant type III polyketide synthase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 947-949.  
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.