scholarly journals A universal pocket in Fatty acyl-AMP ligases ensures redirection of fatty acid pool away from Coenzyme A-based activation

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Gajanan Shrikant Patil ◽  
Priyadarshan Kinatukara ◽  
Sudipta Mondal ◽  
Sakshi Shambhavi ◽  
Ketan D Patel ◽  
...  

Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4'-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3', 5'-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organisations. The universal distribution of FAALs suggests they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.

2017 ◽  
Vol 114 (34) ◽  
pp. 9092-9097 ◽  
Author(s):  
Shi-Hui Dong ◽  
Nicole D. Frane ◽  
Quin H. Christensen ◽  
E. Peter Greenberg ◽  
Rajesh Nagarajan ◽  
...  

In severalProteobacteria, LuxI-type enzymes catalyze the biosynthesis of acyl–homoserine lactones (AHL) signals usingS-adenosyl–l-methionine and either cellular acyl carrier protein (ACP)-coupled fatty acids or CoA–aryl/acyl moieties as progenitors. Little is known about the molecular mechanism of signal biosynthesis, the basis for substrate specificity, or the rationale for donor specificity for any LuxI member. Here, we present several cocrystal structures of BjaI, a CoA-dependent LuxI homolog that represent views of enzyme complexes that exist along the reaction coordinate of signal synthesis. Complementary biophysical, structure–function, and kinetic analysis define the features that facilitate the unusual acyl conjugation withS-adenosylmethionine (SAM). We also identify the determinant that establishes specificity for the acyl donor and identify residues that are critical for acyl/aryl specificity. These results highlight how a prevalent scaffold has evolved to catalyze quorum signal synthesis and provide a framework for the design of small-molecule antagonists of quorum signaling.


2018 ◽  
Vol 84 (10) ◽  
Author(s):  
Marika Ziesack ◽  
Nathan Rollins ◽  
Aashna Shah ◽  
Brendon Dusel ◽  
Gordon Webster ◽  
...  

ABSTRACT Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant Cuphea palustris harbors two distinct TEs: C. palustris FatB1 ( Cp FatB1) (C 8 specificity, lower activity) and Cp FatB2 (C 14 specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C 8 fatty acid production in correlation with improved microbial expression. This chimera led us to identify Cp FatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and in silico docking with ACP, we identified a “positive patch” within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from Cp FatB1 into Cp FatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control. IMPORTANCE Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.


1974 ◽  
Vol 249 (23) ◽  
pp. 7468-7475
Author(s):  
Mark E. Harder ◽  
Ruth C. Ladenson ◽  
Steven D. Schimmel ◽  
David F. Silbert

2013 ◽  
Vol 84 (4-5) ◽  
pp. 549-563 ◽  
Author(s):  
Ian P. Pulsifer ◽  
Christine Lowe ◽  
Swara A. Narayaran ◽  
Alia S. Busuttil ◽  
Sollapura J. Vishwanath ◽  
...  

FEBS Letters ◽  
1989 ◽  
Vol 253 (1-2) ◽  
pp. 221-225 ◽  
Author(s):  
Nicolas Bayan ◽  
Helene Therisod

FEBS Journal ◽  
2015 ◽  
Vol 282 (13) ◽  
pp. 2527-2539 ◽  
Author(s):  
Hui Jiang ◽  
Yue-Yue Wang ◽  
Yuan-Yang Guo ◽  
Jie-Jie Shen ◽  
Xiao-Sheng Zhang ◽  
...  

FEBS Letters ◽  
1994 ◽  
Vol 348 (3) ◽  
pp. 311-316 ◽  
Author(s):  
Ira I.G.S. Verwoert ◽  
Etienne F. Verhagen ◽  
Karin H. van der Linden ◽  
Elizabeth C. Verbree ◽  
H.John J. Nijkamp ◽  
...  

2005 ◽  
Vol 44 (4) ◽  
pp. 620-632 ◽  
Author(s):  
Abraham J. K. Koo ◽  
Martin Fulda ◽  
John Browse ◽  
John B. Ohlrogge

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