A back-door Phenylalanine coordinates the stepwise hexameric loading of acyl carrier protein by the fatty acid biosynthesis enzyme β-hydroxyacyl-acyl carrier protein dehydratase (FabZ)

Shen, Siqi; Hang, Xudong; Zhuang, Jingjing; Zhang, L.; Bi, Hongkai

doi:10.1016/j.ijbiomac.2019.01.094

Cited by 9 publications

(6 citation statements)

References 30 publications

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“…These changes in lipid composition may well be due to a negative regulatory effect of persulfidation of C21 in FabN, the deletion of which is known to impact the biosynthesis of unsaturated fatty acids [ 65 ]. Although there is no structure of Ef FabN, an AlphaFold2 model [ 67 , 68 ] revealed a “hot-dog” fold reminiscent of FabZ hexamers from H. pylori [ 83 ] and P. aeruginosa [ 84 ] and revealed that C21 is located in the α1-β loop, which is highly conserved in FabZs, close to the hot-dog (α3) helix, near the active site glutamate residue and the trimer interface, in this trimer of dimers architecture ( Supplemental Figure S9A ) [ 85 ]. Small displacements of the the α3 helix are known to impact enzyme specificity [ 85 ]; alternatively, persulfidation of C21 may lead to disassembly of the FabN hexamer to dimers and/or influence the way in which holo-ACP engages the hexamer [ 86 ].…”

Section: Discussionmentioning

confidence: 99%

Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis

et al. 2022

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Hydrogen sulfide (H2S) is implicated as a cytoprotective agent that bacteria employ in response to host-induced stressors, such as oxidative stress and antibiotics. The physiological benefits often attributed to H2S, however, are likely a result of downstream, more oxidized forms of sulfur, collectively termed reactive sulfur species (RSS) and including the organic persulfide (RSSH). Here, we investigated the metabolic response of the commensal gut microorganism Enterococcus faecalis to exogenous Na2S as a proxy for H2S/RSS toxicity. We found that exogenous sulfide increases protein abundance for enzymes responsible for the biosynthesis of coenzyme A (CoA). Proteome S-sulfuration (persulfidation), a posttranslational modification implicated in H2S signal transduction, is also widespread in this organism and is significantly elevated by exogenous sulfide in CstR, the RSS sensor, coenzyme A persulfide (CoASSH) reductase (CoAPR) and enzymes associated with de novo fatty acid biosynthesis and acetyl-CoA synthesis. Exogenous sulfide significantly impacts the speciation of fatty acids as well as cellular concentrations of acetyl-CoA, suggesting that protein persulfidation may impact flux through these pathways. Indeed, CoASSH is an inhibitor of E. faecalis phosphotransacetylase (Pta), suggesting that an important metabolic consequence of increased levels of H2S/RSS may be over-persulfidation of this key metabolite, which, in turn, inhibits CoA and acyl-CoA-utilizing enzymes. Our 2.05 Å crystallographic structure of CoA-bound CoAPR provides new structural insights into CoASSH clearance in E. faecalis.

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Section: Discussionmentioning

confidence: 99%

Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis

et al. 2022

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“…Although binding models have been suggested, 5,7,24 no crystal structure of the complex exists and detail on the interactions between actACP and actKR is lacking. Most solved enzyme-ACP complexes 28−41 feature FASs, [28][29][30][31][32][33][34]41 and only two feature a PKS component (namely, KS). 35,36 Moreover, to study protein−substrate interactions, a complex with actACP-1 is required, but this is unfeasible.…”

Section: Jacs Aumentioning

confidence: 99%

“…Although binding models have been suggested, ,, no crystal structure of the complex exists and detail on the interactions between act ACP and act KR is lacking. Most solved enzyme-ACP complexes − feature FASs, − , and only two feature a PKS component (namely, KS). , Moreover, to study protein–substrate interactions, a complex with act ACP- 1 is required, but this is unfeasible. In this work, we combine protein–protein docking, molecular dynamics (MD) simulations, 2D protein-NMR spectroscopy, and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to obtain detailed information on act KR– act ACP binding and act KR–octaketide interactions: our aim is to provide a unified picture of act KR structure and function and address the lack of fundamental knowledge on type II PKSs. ,, …”

Section: Introductionmentioning

confidence: 99%

Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail

Serapian

Crosby

Crump

et al. 2022

JACS Au

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In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes, while covalently tethered to an acyl carrier protein (ACP): this requires the ACP interacting with a series of different enzymes in succession. During biosynthesis of the antibiotic actinorhodin, produced by Streptomyces coelicolor , one such key binding event is between an ACP carrying a 16-carbon octaketide chain ( act ACP) and a ketoreductase ( act KR). Once the octaketide is bound inside act KR, it is likely cyclized between C7 and C12 and regioselective reduction of the ketone at C9 occurs: how these elegant chemical and conformational changes are controlled is not yet known. Here, we perform protein–protein docking, protein NMR, and extensive molecular dynamics simulations to reveal a probable mode of association between act ACP and act KR; we obtain and analyze a detailed model of the C7–C12-cyclized octaketide within the act KR active site; and we confirm this model through multiscale (QM/MM) reaction simulations of the key ketoreduction step. Molecular dynamics simulations show that the most thermodynamically stable cyclized octaketide isomer (7 R ,12 R ) also gives rise to the most reaction competent conformations for ketoreduction. Subsequent reaction simulations show that ketoreduction is stereoselective as well as regioselective, resulting in an S -alcohol. Our simulations further indicate several conserved residues that may be involved in selectivity of C7-12 cyclization and C9 ketoreduction. Detailed insights obtained on ACP-based substrate presentation in type II PKSs can help design ACP-ketoreductase systems with altered regio- or stereoselectivity.

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“…Although binding models have been suggested, 5,7,24 no crystal structure of the complex exists and detail on the interactions between actACP and actKR is lacking. Most solved enzyme-ACP complexes [28][29][30][31][32][33][34][35][36][37][38][39][40] feature FASs, [28][29][30][31][32][33][34] and only two feature a PKS component (namely, ketosynthase). [35][36] Moreover, to study protein-substrate interactions, a complex with actACP-1 is required, but this is unfeasible.…”

Section: Scheme 1 Formation Of Cyclized Octaketide 2 (A) and Subsequent Reactions (B) Amentioning

confidence: 99%

The Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail

Serapian

Crosby

Crump

et al. 2021

Preprint

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In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes whilst covalently tethered to an acyl carrier protein (ACP): this requires the ACP interacting with a series of different enzymes in succession. During biosynthesis of the antibiotic actinorhodin, produced by Streptomyces cœlicolor, one such key binding event is between an ACP carrying a 16-carbon octaketide chain (actACP) and a ketoreductase (actKR). Once the octaketide is bound inside actKR, it is likely cyclized between C7 and C12 and regioselective reduction of the ketone at C9 occurs: how these elegant chemical and conformational changes are controlled is not yet known. Here, we perform protein-protein docking, protein NMR, and extensive molecular dynamics simulations to reveal a likely mode of association between actACP and actKR; we obtain and analyze a detailed model of the C7-C12-cyclized octaketide within actKR’s active site; and confirm this model through multiscale (QM/MM) reaction simulations of the key ketoreduction step. Molecular dynamics simulations show that the most thermodynamically stable cyclized octaketide isomer (7S,12R) also gives rise to the most ‘reactive conformations’ for ketoreduction. Subsequent reaction simulations show that ketoreduction is stereoselective as well as regioselective, resulting in an S-alcohol. Our simulations further indicate several conserved residues that may be involved in selectivity of C7-12 cyclisation and C9 ketoreduction. The detailed insights obtained on ACP-based substrate presentation in type II PKSs will help with the design of nonendogenous ACP-ketoreductase systems capable of biosynthesizing non-natural polyketides.

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A back-door Phenylalanine coordinates the stepwise hexameric loading of acyl carrier protein by the fatty acid biosynthesis enzyme β-hydroxyacyl-acyl carrier protein dehydratase (FabZ)

Cited by 9 publications

References 30 publications

Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis

Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis

Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail

The Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail

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