Volume 15, Issue 10, Pages 1079-1090 (October 2008) Distinct Structural Elements Dictate the Specificity of the Type III Pentaketide Synthase from Neurospora crassa  Sheryl B. Rubin-Pitel, Houjin Zhang, Trang Vu, Joseph S. Brunzelle, Huimin Zhao, Satish K. Nair  Chemistry & Biology  Volume 15, Issue 10, Pages 1079-1090 (October 2008) DOI: 10.1016/j.chembiol.2008.08.011 Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 1 Reaction Schemes of the Synthesis of Polyketides (A) Naringenin chalcone synthesized from 4-coumaroyl-CoA and three molecules of malonyl-CoA by M. sativa CHS. (B) 1,3,6,8-tetrahydroxynaphthalene synthesized from five molecules of malonyl-CoA by S. coelicolor THNS. (C) Myristoyl triketide pyrone synthesized from one molecule of lauroyl-CoA and two molecules of malonyl-CoA by M. tuberculosis Pks18. (D) Stearoyl pentaketide resorcylic acid synthesized from stearoyl-CoA and four molecules of malonyl-CoA by N. crassa ORAS. Enzymatic decarboxylation of resorcylic acid results in the production of the product resorcinol. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 2 Overall Structure of trORAS and Multiple Sequence Alignment (A) Ribbon diagram derived from the crystal structure of trORAS, with one monomer colored in blue and the other colored in magenta. In the lower domain of each monomer, residues Met-189 through Asp-198 form an α-helical insertion that bridges sheets β6 and helix α8. This novel structural element, which has not to our knowledge been previously observed in any type III PKS enzyme, is termed insertion α7i and is shown in yellow. (B) Structure-based sequence alignment of ORAS with other bacterial and plant type III polyketide synthases of note, including M. sativa CHS, M. tuberculosis Pks18, S. coelicolor THNS, and A. arborescens PCS. Residues that constitute the catalytic triad are shown with an asterisk. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 3 Close-Up View of the Active Site of trORAS (A and B) Ribbon diagram of the lower domains of (A) ORAS in blue and (B) CHS in green with bound malonyl-CoA (shown in ball-and-stick representation) highlighting the topological differences in this region of the active site. The α7 insertion present in ORAS is shown in yellow. (C and D) Stick-figure representations of residues that are believed to be involved in catalysis and product/substrate specificity in the active sites of (C) ORAS and (D) CHS complexed with naringenin. The phenylalanine residues that function as steric gates to control specificity are colored in blue, and residues that are implicated in participating in mechanistic steering of intermediates are shown in orange. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 4 Overview of Reactions Catalyzed by trORAS and the Phe-252→Gly Mutant Products confirmed by LC-MS/MS for trORAS are shown in red, those for the Phe-252→Gly mutant are shown in blue, and products observed for both enzymes are shown in green. Mass spectral analysis of these products is provided in Table S2. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 5 Active Sites of trORAS and the Phe-252→Gly Mutant (A) Electron density map (shown in blue mesh and contoured at 2.5σ) calculated using Fourier coefficients Fobs − Fcalc with phases derived from the final refined model of Phe-252→Gly trORAS minus the atoms of residue Gly-252 and all active site ligands. Clear, but discontinuous, electron density can be observed near the vicinity of Gly-252 and has been modeled as a molecule of polyethylene glycol. The final refined coordinates of important active site residues are shown as stick figures, the polyethylene glycol is shown in pink. (B) A superposition of active site residues of wild-type trORAS (shown in pink) and the Phe-252→Gly variant (shown in blue). There are no significant changes in the main-chain atoms of the two structures and only small alterations in the position of the active site residues are shown. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 6 Close-Up View of the Active Site of trORAS Bound to Eicosanoic Acid (A and B) Orthogonal views of an electron density map (shown in blue mesh and contoured at 2σ) calculated using Fourier coefficients Fobs − Fcalc with phases derived from the final refined model of the ORAS-eicosanoic acid complex minus the atoms of the eicosanoic acid ligand. The final refined coordinates of important active site residues are shown as stick figures, the eicosanonic acid is shown in pink, and the α7 insertion is shown as a ribbon diagram in red. (C–E) Ribbon diagrams derived from the crystal structures of (C) trORAS (shown in blue) with bound eicosanoic acid, (D) Pks18 (shown in cyan) with bound myristic acid, and (E) THNS (shown in pink) with a bound molecule of polyethylene glycol. Each of the ligands is shown as CPK models and the respective active site cysteine residues are shown in ball-and-stick representation. Chemistry & Biology 2008 15, 1079-1090DOI: (10.1016/j.chembiol.2008.08.011) Copyright © 2008 Elsevier Ltd Terms and Conditions