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PDBsum entry 3hrq

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Biosynthetic protein PDB id
3hrq
Jmol
Contents
Protein chains
317 a.a. *
Ligands
PLM ×2
Waters ×458
* Residue conservation analysis
PDB id:
3hrq
Name: Biosynthetic protein
Title: The product template domain from pksa with palmitate bound
Structure: Aflatoxin biosynthesis polyketide synthase. Chain: a, b. Fragment: unp residues 1305-1660. Synonym: pks. Engineered: yes
Source: Aspergillus parasiticus. Organism_taxid: 5067. Gene: pksa, pksl1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.203     R-free:   0.223
Authors: T.P.Korman,S.C.Tsai
Key ref:
J.M.Crawford et al. (2009). Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization. Nature, 461, 1139-1143. PubMed id: 19847268 DOI: 10.1038/nature08475
Date:
09-Jun-09     Release date:   20-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q12053  (PKSL1_ASPPA) -  Noranthrone synthase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2109 a.a.
317 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.221  - Noranthrone synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 7 malonyl-CoA + hexanoyl-[acyl-carrier protein] = 7 CoA + norsolorinate anthrone + [acyl-carrier protein] + 7 CO2 + 2 H2O
7 × malonyl-CoA
+ hexanoyl-[acyl-carrier protein]
= 7 × CoA
+ norsolorinate anthrone
+ [acyl-carrier protein]
+ 7 × CO(2)
+ 2 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/nature08475 Nature 461:1139-1143 (2009)
PubMed id: 19847268  
 
 
Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization.
J.M.Crawford, T.P.Korman, J.W.Labonte, A.L.Vagstad, E.A.Hill, O.Kamari-Bidkorpeh, S.C.Tsai, C.A.Townsend.
 
  ABSTRACT  
 
Polyketides are a class of natural products with diverse structures and biological activities. The structural variability of aromatic products of fungal nonreducing, multidomain iterative polyketide synthases (NR-PKS group of IPKSs) results from regiospecific cyclizations of reactive poly-beta-keto intermediates. How poly-beta-keto species are synthesized and stabilized, how their chain lengths are determined, and, in particular, how specific cyclization patterns are controlled have been largely inaccessible and functionally unknown until recently. A product template (PT) domain is responsible for controlling specific aldol cyclization and aromatization of these mature polyketide precursors, but the mechanistic basis is unknown. Here we present the 1.8 A crystal structure and mutational studies of a dissected PT monodomain from PksA, the NR-PKS that initiates the biosynthesis of the potent hepatocarcinogen aflatoxin B(1) in Aspergillus parasiticus. Despite having minimal sequence similarity to known enzymes, the structure displays a distinct 'double hot dog' (DHD) fold. Co-crystal structures with palmitate or a bicyclic substrate mimic illustrate that PT can bind both linear and bicyclic polyketides. Docking and mutagenesis studies reveal residues important for substrate binding and catalysis, and identify a phosphopantetheine localization channel and a deep two-part interior binding pocket and reaction chamber. Sequence similarity and extensive conservation of active site residues in PT domains suggest that the mechanistic insights gleaned from these studies will prove general for this class of IPKSs, and lay a foundation for defining the molecular rules controlling NR-PKS cyclization specificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Biosynthesis of norsolorinic acid anthrone (1) by PksA. a, Native catalytic cycle. The SAT domain in PksA selects a hexanoyl starter unit. The MAT domain loads the free ACP with malonyl units. After seven successive condensation events with malonyl-ACP catalysed in KS, the linear ACP-bound polyketide 6 is cyclized (C4–C9 and C2–C11 cyclization events) and aromatized in the product template (PT) domain to give the bicyclic intermediate 7. The TE catalyses C-C cyclization to release anthrone 1, which undergoes oxidation to the anthraquinone norsolorinic acid (2), to initiate the complex biosynthetic pathway to aflatoxin B[1] (3). Asterisks denote the C and O nucleophiles involved in on-path and off-path cyclizations, respectively. b, In the absence of TE, the PT product 7 undergoes spontaneous O-C cyclization to norpyrone (4). The PT monodomain structure was solved with intermediate/product mimic 5 (HC8). c, Conversions from 6 to 7 via intermediates 8, 9 and 10.
Figure 4.
Figure 4: Proposed mechanism of cyclizations catalysed by the PT domain. For clarity of presentation, liberties have been taken with the relative placement of active-site residues, but the principal interactions with the fully extended polyketide intermediate (left) are depicted, notably, to ordered crystallographic water molecules and a slight 'kink' towards the cyclization chamber. Hydrogens indicated by dotted circles form hydrogen bonds to acceptors on the catalytic Asp 1543. The His 1345/Asp 1543 catalytic dyad acts as the catalytic base, leading to enolate formation at C4 to initiate first ring cyclization (C4–C9). The second ring is formed in the same manner as the first to achieve C2–C11 closure (Supplementary Fig. 3).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2009, 461, 1139-1143) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21102597 T.Saruwatari, A.P.Praseuth, M.Sato, K.Torikai, H.Noguchi, and K.Watanabe (2011).
A comprehensive overview on genomically directed assembly of aromatic polyketides and macrolide lactones using fungal megasynthases.
  J Antibiot (Tokyo), 64, 9.  
20358042 H.Zhou, Y.Li, and Y.Tang (2010).
Cyclization of aromatic polyketides from bacteria and fungi.
  Nat Prod Rep, 27, 839-868.  
20203700 I.Fujii (2010).
Functional analysis of fungal polyketide biosynthesis genes.
  J Antibiot (Tokyo), 63, 207-218.  
20601982 I.Molnár, D.M.Gibson, and S.B.Krasnoff (2010).
Secondary metabolites from entomopathogenic Hypocrealean fungi.
  Nat Prod Rep, 27, 1241-1275.  
20578001 J.Huffman, R.Gerber, and L.Du (2010).
Recent advancements in the biosynthetic mechanisms for polyketide-derived mycotoxins.
  Biopolymers, 93, 764-776.  
21079635 J.M.Crawford, and C.A.Townsend (2010).
New insights into the formation of fungal aromatic polyketides.
  Nat Rev Microbiol, 8, 879-889.  
20861892 J.M.Crawford, and J.Clardy (2010).
Biosynthesis: not just passing through.
  Nat Chem, 2, 805-807.  
20532365 J.M.Gao, J.C.Qin, G.Pescitelli, S.Di Pietro, Y.T.Ma, and A.L.Zhang (2010).
Structure and absolute configuration of toxic polyketide pigments from the fruiting bodies of the fungus Cortinarius rufo-olivaceus.
  Org Biomol Chem, 8, 3543-3551.  
20552126 K.M.Fisch, E.Skellam, D.Ivison, R.J.Cox, A.M.Bailey, C.M.Lazarus, and T.J.Simpson (2010).
Catalytic role of the C-terminal domains of a fungal non-reducing polyketide synthase.
  Chem Commun (Camb), 46, 5331-5333.  
20111804 L.Du, and L.Lou (2010).
PKS and NRPS release mechanisms.
  Nat Prod Rep, 27, 255-278.  
20332208 T.P.Korman, J.M.Crawford, J.W.Labonte, A.G.Newman, J.Wong, C.A.Townsend, and S.C.Tsai (2010).
Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis.
  Proc Natl Acad Sci U S A, 107, 6246-6251.
PDB code: 3ils
20534347 W.Ding, C.Lei, Q.He, Q.Zhang, Y.Bi, and W.Liu (2010).
Insights into bacterial 6-methylsalicylic acid synthase and its engineering to orsellinic acid synthase for spirotetronate generation.
  Chem Biol, 17, 495-503.  
20534346 Y.H.Chooi, R.Cacho, and Y.Tang (2010).
Identification of the viridicatumtoxin and griseofulvin gene clusters from Penicillium aethiopicum.
  Chem Biol, 17, 483-494.  
20361326 Y.M.Chiang, B.R.Oakley, N.P.Keller, and C.C.Wang (2010).
Unraveling polyketide synthesis in members of the genus Aspergillus.
  Appl Microbiol Biotechnol, 86, 1719-1736.  
20336235 Z.X.Liang (2010).
Complexity and simplicity in the biosynthesis of enediyne natural products.
  Nat Prod Rep, 27, 499-528.  
19847256 D.H.Sherman (2009).
Biochemistry: Enzyme's black box cracked open.
  Nature, 461, 1068-1069.  
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 code is shown on the right.