Structural Insight into the Enzymatic Formation of Bacterial Stilbene Takahiro Mori, Takayoshi Awakawa, Koichiro Shimomura, Yuri Saito, Dengfeng Yang, Hiroyuki Morita, Ikuro Abe  Cell Chemical Biology  Volume 23, Issue 12, Pages 1468-1479 (December 2016) DOI: 10.1016/j.chembiol.2016.10.010 Copyright © 2016 Elsevier Ltd Terms and Conditions

Cell Chemical Biology 2016 23, 1468-1479DOI: (10. 1016/j. chembiol Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 Enzymatic Formation of Stilbenes and Dialkylresorcinols Reaction schemes for (A) the synthesis of resveratrol by STS, (B) the synthesis of dialkylresorcinols by C. pinensis DarB and DarA, and (C) the proposed synthesis of bacterial stilbene by P. luminescens StlD and StlC. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 In Vitro Enzymatic Activities of P. luminescens StlD and StlC (A) HPLC elution profiles of enzyme reaction products of P. luminescens StlD and StlC from 5-phenyl-2,4-pentadienoyl-SNAC (4) and isovaleryl β-ketoacyl-SNAC (5). HPLC elution profiles of (B) the enzyme reaction products of P. luminescens StlD and StlC from the α,β-unsaturated-acyl substrate analogs 7 and 8, and (C) the enzyme reaction products of P. luminescens StlD from the β-ketoacyl substrate analogs 14–19. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Comparisons of the Active Site Structures of P. luminescens StlD and Other β-ketosynthases The active site cavities of (A) P. luminescens StlD, (B) X. campestris OleA, (C) M. fulvus MxnB, (D) C. coralloides CorB, (E) the H302A mutant of StlD, and (F) the superimposed view of the apo and H302A mutant structures. The acyl-binding pocket, the second acyl-binding pocket, and the elongation/cyclization pocket are highlighted in orange, blue, and green, respectively. The cerulenin molecule in X. campestris OleA is shown as a white stick model. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Structure-Based Mutagenesis Experiments of P. luminescens StlD HPLC elution profiles of the enzymatic reaction products by wild-type StlD and its H302A, C126A, and E154Q mutant enzymes. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 Close-Up Views of the Active Site Cavity of P. luminescens StlD with the β-Ketoacyl Intermediate Covalently Bound to Cys126 (A) Close-up views of the active site cavity of the StlD apo and complex structure of StlD with the isovaleryl β-ketoacyl moiety at Cys126. (B) The interactions between the isovaleryl β-ketoacyl moiety and active site residues. (C) Stereo view of the active site of the complex structure of StlD with the isovaleryl β-ketoacyl substrate. The active site residues in the complex structure and the apo structure are colored in magenta and green, respectively. The isovaleryl β-ketoacyl moiety in P. luminescens StlD is depicted by a blue stick model. The simulated annealing omitting |Fo − Fc| electron density maps contoured at +3.0 sigma are displayed as gray meshes. The water molecules and the hydrogen bonds are indicated with red spheres and yellow dotted lines, respectively. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 6 Schematic Representations of the Proposed Mechanism for the P. luminescens StlD Enzyme Reaction The proposed mechanism of the StlD-catalyzed one-pot formation of the CHD scaffold. (A) The β-ketoacyl moiety, loaded onto the catalytic Cys126, rotates toward the short acyl-binding pocket. (B) The basic residue Glu154 abstracts a proton from the γ-carbon of the enzyme-bound β-ketoacyl unit, and then Claisen condensation between the β-ketoacyl unit and the second α,β-saturated-acyl substrate generates the branched intermediate. (C) Keto-enol tautomerization reactivates the catalytic Glu154. (D) The Michael addition of the β-ketoacyl moiety to the β-carbon of the α,β-saturated-acyl unit produces the carboxy-CHD scaffold. (E) An activated nucleophilic water molecule cleaves the thioester bond of the enzyme-bound intermediate. (F) Keto-enol tautomerization reactivates the catalytic Glu154. White open arrows indicate the active site entrance. Cell Chemical Biology 2016 23, 1468-1479DOI: (10.1016/j.chembiol.2016.10.010) Copyright © 2016 Elsevier Ltd Terms and Conditions