1
|
Hasan SMN, Lou JW, Keszei AFA, Dai DL, Mazhab-Jafari MT. Atomic model for core modifying region of human fatty acid synthase in complex with Denifanstat. Nat Commun 2023; 14:3460. [PMID: 37308485 DOI: 10.1038/s41467-023-39266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Fatty acid synthase (FASN) catalyzes the de novo synthesis of palmitate, a 16-carbon chain fatty acid that is the primary precursor of lipid metabolism and an important intracellular signaling molecule. FASN is an attractive drug target in diabetes, cancer, fatty liver diseases, and viral infections. Here, we develop an engineered full-length human FASN (hFASN) that enables isolation of the condensing and modifying regions of the protein post-translation. The engineered protein enables electron cryo-microscopy (cryoEM) structure determination of the core modifying region of hFASN to 2.7 Å resolution. Examination of the dehydratase dimer within this region reveals that unlike its close homolog, porcine FASN, the catalytic cavity is close-ended and is accessible only through one opening in the vicinity of the active site. The core modifying region exhibits two major global conformational variabilities that describe long-range bending and twisting motions of the complex in solution. Finally, we solved the structure of this region bound to an anti-cancer drug, Denifanstat (i.e., TVB-2640), demonstrating the utility of our approach as a platform for structure guided design of future hFASN small molecule inhibitors.
Collapse
Affiliation(s)
- S M Naimul Hasan
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer W Lou
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - David L Dai
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mohammad T Mazhab-Jafari
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
| |
Collapse
|
2
|
Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
Collapse
Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
3
|
Yun CS, Nishimoto K, Motoyama T, Shimizu T, Hino T, Dohmae N, Nagano S, Osada H. Unique features of the ketosynthase domain in a nonribosomal peptide synthetase-polyketide synthase hybrid enzyme, tenuazonic acid synthetase 1. J Biol Chem 2020; 295:11602-11612. [PMID: 32565425 DOI: 10.1074/jbc.ra120.013105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/18/2020] [Indexed: 11/06/2022] Open
Abstract
Many microbial secondary metabolites are produced by multienzyme complexes comprising nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). The ketosynthase (KS) domains of polyketide synthase normally catalyze the decarboxylative Claisen condensation of acyl and malonyl blocks to extend the polyketide chain. However, the terminal KS domain in tenuazonic acid synthetase 1 (TAS1) from the fungus Pyricularia oryzae conducts substrate cyclization. Here, we report on the unique features of the KS domain in TAS1. We observed that this domain is monomeric, not dimeric as is typical for KSs. Analysis of a 1.68-Å resolution crystal structure suggests that the substrate cyclization is triggered via proton abstraction from the active methylene moiety in the substrate by a catalytic His-322 residue. Additionally, we show that TAS1 KS promiscuously accepts aminoacyl substrates and that this promiscuity can be increased by a single amino acid substitution in the substrate-binding pocket of the enzyme. These findings provide insight into a KS domain that accepts the amino acid-containing substrate in an NRPS-PKS hybrid enzyme and provide hints to the substrate cyclization mechanism performed by the KS domain in the biosynthesis of the mycotoxin tenuazonic acid.
Collapse
Affiliation(s)
- Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Kazuki Nishimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| |
Collapse
|
4
|
Rittner A, Paithankar KS, Drexler DJ, Himmler A, Grininger M. Probing the modularity of megasynthases by rational engineering of a fatty acid synthase Type I. Protein Sci 2018; 28:414-428. [PMID: 30394635 DOI: 10.1002/pro.3550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022]
Abstract
Modularity is a fundamental property of megasynthases such as polyketide synthases (PKSs). In this study, we exploit the close resemblance between PKSs and animal fatty acid synthase (FAS) to re-engineer animal FAS to probe the modularity of the FAS/PKS family. Guided by sequence and structural information, we truncate and dissect animal FAS into its components, and reassemble them to generate new PKS-like modules as well as bimodular constructs. The novel re-engineered modules resemble all four common types of PKSs and demonstrate that this approach can be a powerful tool to deliver products with higher catalytic efficiency. Our data exemplify the inherent plasticity and robustness of the overall FAS/PKS fold, and open new avenues to explore FAS-based biosynthetic pathways for custom compound design.
Collapse
Affiliation(s)
- Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Karthik S Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - David Jan Drexler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Aaron Himmler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| |
Collapse
|
5
|
Lefebvre C, Boulon R, Ducoux M, Gavalda S, Laval F, Jamet S, Eynard N, Lemassu A, Cam K, Bousquet MP, Bardou F, Burlet-Schiltz O, Daffé M, Quémard A. HadD, a novel fatty acid synthase type II protein, is essential for alpha- and epoxy-mycolic acid biosynthesis and mycobacterial fitness. Sci Rep 2018; 8:6034. [PMID: 29662082 PMCID: PMC5902629 DOI: 10.1038/s41598-018-24380-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/03/2018] [Indexed: 02/05/2023] Open
Abstract
Mycolic acids (MAs) have a strategic location within the mycobacterial envelope, deeply influencing its architecture and permeability, and play a determinant role in the pathogenicity of mycobacteria. The fatty acid synthase type II (FAS-II) multienzyme system is involved in their biosynthesis. A combination of pull-downs and proteomics analyses led to the discovery of a mycobacterial protein, HadD, displaying highly specific interactions with the dehydratase HadAB of FAS-II. In vitro activity assays and homology modeling showed that HadD is, like HadAB, a hot dog folded (R)-specific hydratase/dehydratase. A hadD knockout mutant of Mycobacterium smegmatis produced only the medium-size alpha’-MAs. Data strongly suggest that HadD is involved in building the third meromycolic segment during the late FAS-II elongation cycles, leading to the synthesis of the full-size alpha- and epoxy-MAs. The change in the envelope composition induced by hadD inactivation strongly altered the bacterial fitness and capacities to aggregate, assemble into colonies or biofilms and spread by sliding motility, and conferred a hypersensitivity to the firstline antimycobacterial drug rifampicin. This showed that the cell surface properties and the envelope integrity were greatly affected. With the alarmingly increasing case number of nontuberculous mycobacterial diseases, HadD appears as an attractive target for drug development.
Collapse
Affiliation(s)
- Cyril Lefebvre
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Richard Boulon
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Manuelle Ducoux
- Département Biologie Structurale & Biophysique, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Sabine Gavalda
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Françoise Laval
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Stevie Jamet
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Nathalie Eynard
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Anne Lemassu
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Kaymeuang Cam
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Marie-Pierre Bousquet
- Département Biologie Structurale & Biophysique, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Fabienne Bardou
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Odile Burlet-Schiltz
- Département Biologie Structurale & Biophysique, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Mamadou Daffé
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France
| | - Annaïk Quémard
- Département Tuberculose & Biologie des Infections, Institut de Pharmacologie et de Biologie Structurale, UMR5089, Université de Toulouse, CNRS, UPS, 31077, Toulouse Cedex 04, France.
| |
Collapse
|
6
|
Faille A, Gavalda S, Slama N, Lherbet C, Maveyraud L, Guillet V, Laval F, Quémard A, Mourey L, Pedelacq JD. Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases. J Mol Biol 2017; 429:1554-1569. [PMID: 28377293 DOI: 10.1016/j.jmb.2017.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 02/04/2023]
Abstract
Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacterium tuberculosis catalyzes key biosynthetic steps of lipid virulence factors phthiocerol dimycocerosates and phenolic glycolipids. Given the insolubility of the natural C28-C30 fatty acyl substrate of the PpsC dehydratase (DH) domain, we investigated its structure-function relationships in the presence of shorter surrogate substrates. Since most enzymes belonging to the (R)-specific enoyl hydratase/hydroxyacyl dehydratase family conduct the reverse hydration reaction in vitro, we have determined the X-ray structures of the PpsC DH domain, both unliganded (apo) and in complex with trans-but-2-enoyl-CoA or trans-dodec-2-enoyl-CoA derivatives. This study provides for the first time a snapshot of dehydratase-ligand interactions following a hydration reaction. Our structural analysis allowed us to identify residues essential for substrate binding and activity. The structural comparison of the two complexes also sheds light on the need for long acyl chains for this dehydratase to carry out its function, consistent with both its in vitro catalytic behavior and the physiological role of the PpsC enzyme.
Collapse
Affiliation(s)
- Alexandre Faille
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Nawel Slama
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
| |
Collapse
|
7
|
Xie X, Garg A, Khosla C, Cane DE. Mechanism and Stereochemistry of Polyketide Chain Elongation and Methyl Group Epimerization in Polyether Biosynthesis. J Am Chem Soc 2017; 139:3283-3292. [PMID: 28157306 DOI: 10.1021/jacs.7b00278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyketide synthases responsible for the biosynthesis of the polyether antibiotics nanchangmycin (1) and salinomycin (4) harbor a number of redox-inactive ketoreductase (KR0) domains that are implicated in the generation of C2-epimerized (2S)-2-methyl-3-ketoacyl-ACP intermediates. Evidence that the natural substrate for the polyether KR0 domains is, as predicted, a (2R)-2-methyl-3-ketoacyl-ACP intermediate, came from a newly developed coupled ketosynthase (KS)-ketoreductase (KR) assay that established that the decarboxylative condensation of methylmalonyl-CoA with S-propionyl-N-acetylcysteamine catalyzed by the Nan[KS1][AT1] didomain from module 1 of the nanchangmycin synthase generates exclusively the corresponding (2R)-2-methyl-3-ketopentanoyl-ACP (7a) product. In tandem equilibrium isotope exchange experiments, incubation of [2-2H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-ACP (6a) with redox-active, epimerase-inactive EryKR6 from module 6 of the 6-deoxyerythronolide B synthase and catalytic quantities of NADP+ in the presence of redox-inactive, recombinant NanKR10 or NanKR50, from modules 1 and 5 of the nanchangmycin synthase, or recombinant SalKR70 from module 7 of the salinomycin synthase, resulted in first-order, time-dependent washout of deuterium from 6a. Control experiments confirmed that this washout was due to KR0-catalyzed isotope exchange of the reversibly generated, transiently formed oxidation product [2-2H]-(2R)-2-methyl-3-ketopentanoyl-ACP (7a), consistent with the proposed epimerase activity of each of the KR0 domains. Although they belong to the superfamily of short chain dehydrogenase-reductases, the epimerase-active KR0 domains from polyether synthases lack one or both residues of the conserved Tyr-Ser dyad that has previously been implicated in KR-catalyzed epimerizations.
Collapse
Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| |
Collapse
|
8
|
Garg A, Xie X, Keatinge-Clay A, Khosla C, Cane DE. Elucidation of the cryptic epimerase activity of redox-inactive ketoreductase domains from modular polyketide synthases by tandem equilibrium isotope exchange. J Am Chem Soc 2014; 136:10190-3. [PMID: 25004372 PMCID: PMC4111212 DOI: 10.1021/ja5056998] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Many modular polyketide synthases
harbor one or more redox-inactive
domains of unknown function that are highly homologous to ketoreductase
(KR) domains. A newly developed tandem equilibrium isotope exchange
(EIX) assay has now established that such “KR0”
domains catalyze the biosynthetically essential epimerization of transient
(2R)-2-methyl-3-ketoacyl-ACP intermediates to the
corresponding (2S)-2-methyl-3-ketoacyl-ACP diastereomers.
Incubation of [2-2H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP ([2-2H]-3b) with the EryKR30 domain from module 3 of the
6-deoxyerythronolide B synthase, and the redox-active,
nonepimerizing EryKR6 domain and NADP+ resulted in time-
and cofactor-dependent washout of deuterium from 3b,
as a result of EryKR30-catalyzed epimerization of transiently
generated [2-2H]-2-methyl-3-ketopentanoyl-ACP (4). Similar results were obtained with redox-inactive PicKR30 from module 3 of the picromycin synthase. Four redox-inactive mutants
of epimerase-active EryKR1 were engineered by mutagenesis of the NADPH
binding site of this enzyme. Tandem EIX established that these EryKR10 mutants retained the intrinsic epimerase activity of the
parent EryKR1 domain. These results establish the intrinsic epimerase
activity of redox-inactive KR0 domains, rule out any role
for the NADPH cofactor in epimerization, and provide a general experimental
basis for decoupling the epimerase and reductase activities of a large
class of PKS domains.
Collapse
Affiliation(s)
- Ashish Garg
- Department of Chemistry, Box H, Brown University , Providence, Rhode Island 02912-9108, United States
| | | | | | | | | |
Collapse
|
9
|
Probing the selectivity and protein·protein interactions of a nonreducing fungal polyketide synthase using mechanism-based crosslinkers. ACTA ACUST UNITED AC 2013; 20:1135-46. [PMID: 23993461 DOI: 10.1016/j.chembiol.2013.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 01/05/2023]
Abstract
Protein·protein interactions, which often involve interactions among an acyl carrier protein (ACP) and ACP partner enzymes, are important for coordinating polyketide biosynthesis. However, the nature of such interactions is not well understood, especially in the fungal nonreducing polyketide synthases (NR-PKSs) that biosynthesize toxic and pharmaceutically important polyketides. Here, we employ mechanism-based crosslinkers to successfully probe ACP and ketosynthase (KS) domain interactions in NR-PKSs. We found that crosslinking efficiency is closely correlated with the strength of ACP·KS interactions and that KS demonstrates strong starter unit selectivity. We further identified positively charged surface residues by KS mutagenesis, which mediates key interactions with the negatively charged ACP surface. Such complementary/matching contact pairs can serve as "adapter surfaces" for future efforts to generate new polyketides using NR-PKSs.
Collapse
|
10
|
Oyola-Robles D, Gay DC, Trujillo U, Sánchez-Parés JM, Bermúdez ML, Rivera-Díaz M, Carballeira NM, Baerga-Ortiz A. Identification of novel protein domains required for the expression of an active dehydratase fragment from a polyunsaturated fatty acid synthase. Protein Sci 2013; 22:954-63. [PMID: 23696301 DOI: 10.1002/pro.2278] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 01/08/2023]
Abstract
Polyunsaturated fatty acids (PUFAs) are made in some strains of deep-sea bacteria by multidomain proteins that catalyze condensation, ketoreduction, dehydration, and enoyl-reduction. In this work, we have used the Udwary-Merski Algorithm sequence analysis tool to define the boundaries that enclose the dehydratase (DH) domains in a PUFA multienzyme. Sequence analysis revealed the presence of four areas of high structure in a region that was previously thought to contain only two DH domains as defined by FabA-homology. The expression of the protein fragment containing all four protein domains resulted in an active enzyme, while shorter protein fragments were not soluble. The tetradomain fragment was capable of catalyzing the conversion of crotonyl-CoA to β-hydroxybutyryl-CoA efficiently, as shown by UV absorbance change as well as by chromatographic retention of reaction products. Sequence alignments showed that the two novel domains contain as much sequence conservation as the FabA-homology domains, suggesting that they too may play a functional role in the overall reaction. Structure predictions revealed that all domains belong to the hotdog protein family: two of them contain the active site His70 residue present in FabA-like DHs, while the remaining two do not. Replacing the active site His residues in both FabA domains for Ala abolished the activity of the tetradomain fragment, indicating that the DH activity is contained within the FabA-homology regions. Taken together, these results provide a first glimpse into a rare arrangement of DH domains which constitute a defining feature of the PUFA synthases.
Collapse
Affiliation(s)
- Delise Oyola-Robles
- Department of Biochemistry, University of Puerto Rico School of Medicine, San Juan, 00936-5067, Puerto Rico
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT. Divergence of multimodular polyketide synthases revealed by a didomain structure. Nat Chem Biol 2012; 8:615-21. [PMID: 22634636 PMCID: PMC3477503 DOI: 10.1038/nchembio.964] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 03/30/2012] [Indexed: 01/15/2023]
Abstract
The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues.
Collapse
Affiliation(s)
- Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin
| | - Darren C. Gay
- Department of Chemistry and Biochemistry, The University of Texas at Austin
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio
| | - Mark A. White
- Sealy Center for Structural and Molecular Biophysics, UTMB Galveston
| | | |
Collapse
|
12
|
Mammalian fatty acid synthase activity from crude tissue lysates tracing ¹³C-labeled substrates using gas chromatography-mass spectrometry. Anal Biochem 2012; 428:158-66. [PMID: 22728958 DOI: 10.1016/j.ab.2012.06.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 01/08/2023]
Abstract
Fatty acid synthase (FASN or FAS, EC 2.3.1.85) is the sole mammalian enzyme to synthesize fatty acids de novo from acetyl- and malonyl-coenzyme A (CoA) esters. This article describes a new method that directly quantifies uniformly labeled (¹³C₁₆-labeled palmitate ([¹³C₁₆]palmitate) by tracing [¹³C₂]acetyl-CoA and [¹³C₃]malonyl-CoA using an in vitro FASN assay. This method used gas chromatography-mass spectrometry (GC-MS) to detect [¹³C₁₆]palmitate carboxylate anions (m/z 271) of pentafluorobenzyl (PFB) derivatives and was highly sensitive at femtomole quantities. Uniformly incorporated [¹³C₁₆]palmitate was the primary product of both recombinant and crude tissue lysate FASN. Quantification of FASN protein within crude tissue lysates ensured equal FASN amounts, preserved steady-state kinetics, and enabled calculation of FASN-specific activity. FASN activity determined by [¹³C₁₆]palmitate synthesis was consistent with values obtained from β-nicotinamide adenine dinucleotide 2'-phosphate (NADPH) oxidation assays. Analysis of FASN activity from tissue extracts was not hampered by contaminating enzymes or preexisting fatty acids. Crude mammary gland and liver lysates had significantly different activities at 82 and 65 nmol min⁻¹ mg⁻¹, respectively, suggesting that tissue-specific activity levels differ in a manner unrelated to FASN amount. GC-MS quantification of [¹³C₁₆]palmitate synthesis permits sensitive evaluation of FASN activity from tissues of varied physiological states and of purified FASN activity in the presence of modifying proteins, enzymes, or drugs.
Collapse
|
13
|
Abstract
The enoyl-acyl carrier protein reductase (ENR) is the last enzyme in the fatty acid elongation cycle. Unlike most enzymes in this essential pathway, ENR displays an unusual diversity among organisms. The growing interest in ENRs is mainly due to the fact that a variety of both synthetic and natural antibacterial compounds are shown to specifically target their activity. The primary anti-tuberculosis drug, isoniazid, and the broadly used antibacterial compound, triclosan, both target this enzyme. In this review, we discuss the diversity of ENRs, and their inhibitors in the light of current research progress.
Collapse
Affiliation(s)
- R. P. Massengo-Tiassé
- Departments of Microbiology, B103, Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL 61801 USA
| | - J. E. Cronan
- Departments of Microbiology, B103, Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| |
Collapse
|
14
|
Abstract
This chapter describes structural and associated enzymological studies of polyketide synthases, including isolated single domains and multidomain fragments. The sequence-structure-function relationship of polyketide biosynthesis, compared with homologous fatty acid synthesis, is discussed in detail. Structural enzymology sheds light on sequence and structural motifs that are important for the precise timing, substrate recognition, enzyme catalysis, and protein-protein interactions leading to the extraordinary structural diversity of naturally occurring polyketides.
Collapse
|
15
|
Keatinge-Clay A. Crystal structure of the erythromycin polyketide synthase dehydratase. J Mol Biol 2008; 384:941-53. [PMID: 18952099 PMCID: PMC3496180 DOI: 10.1016/j.jmb.2008.09.084] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 09/14/2008] [Accepted: 09/29/2008] [Indexed: 01/07/2023]
Abstract
The dehydratases (DHs) of modular polyketide synthases (PKSs) catalyze dehydrations that occur frequently in the biosynthesis of complex polyketides, yet little is known about them structurally or mechanistically. Here, the structure of a DH domain, isolated from the fourth module of the erythromycin PKS, is presented at 1.85 A resolution. As with the DH of the highly related animalian fatty acid synthase, the DH monomer possesses a double-hotdog fold. Two symmetry mates within the crystal lattice make a contact that likely represents the DH dimerization interface within an intact PKS. Conserved hydrophobic residues on the DH surface indicate potential interfaces with two other PKS domains, the ketoreductase and the acyl carrier protein. Mutation of an invariant arginine at the hypothesized acyl carrier protein docking site in the context of the erythromycin PKS resulted in decreased production of the erythromycin precursor 6-deoxyerythronolide B. The structure elucidates how the alpha-hydrogen and beta-hydroxyl group of a polyketide substrate interact with the catalytic histidine and aspartic acid in the DH active site prior to dehydration.
Collapse
Affiliation(s)
- Adrian Keatinge-Clay
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16 Street, San Francisco, California 94158
| |
Collapse
|
16
|
|
17
|
Vázquez MJ, Leavens W, Liu R, Rodríguez B, Read M, Richards S, Winegar D, Domínguez JM. Discovery of GSK837149A, an inhibitor of human fatty acid synthase targeting the beta-ketoacyl reductase reaction. FEBS J 2008; 275:1556-1567. [PMID: 18312417 DOI: 10.1111/j.1742-4658.2008.06314.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GSK837149A has been identified as a selective inhibitor of human fatty acid synthase (FAS). The compound was first isolated as a minor impurity in a sample found to be active against the enzyme in a high-throughput screening campaign. The structure of this compound was confirmed by NMR and MS studies, and evaluation of the newly synthesized molecule confirmed its activity against FAS. The compound and other analogs synthesized, all being symmetrical structures containing a bisulfonamide urea, act by inhibiting the beta-ketoacyl reductase activity of the enzyme. GSK837149A inhibits FAS in a reversible mode, with a K(i) value of approximately 30 nm, and it possibly binds to the enzyme-ketoacyl-ACP complex. Although initial results suggest that cell penetration for these compounds is impaired, they still can be regarded as useful tools with which to probe and explore the beta-ketoacyl reductase active site in FAS, helping in the design of new inhibitors.
Collapse
Affiliation(s)
- María Jesús Vázquez
- GlaxoSmithKline R&D, Biological Reagents and Assay Development Department, Centro de Investigación Básica, Tres Cantos, Spain
| | - William Leavens
- GlaxoSmithKline R&D, Analytical Chemistry Department, Medicines Research Center, Stevenage, UK
| | - Ronggang Liu
- GlaxoSmithKline R&D, Cardiovascular and Urogenital Centre of Excellence for Drug Discovery, King of Prussia, PA, USA
| | - Beatriz Rodríguez
- GlaxoSmithKline R&D, Biological Reagents and Assay Development Department, Centro de Investigación Básica, Tres Cantos, Spain
| | - Martin Read
- GlaxoSmithKline R&D, Analytical Chemistry Department, Medicines Research Center, Stevenage, UK
| | - Stephen Richards
- GlaxoSmithKline R&D, Analytical Chemistry Department, Medicines Research Center, Stevenage, UK
| | - Deborah Winegar
- GlaxoSmithKline R&D, Metabolic Centre of Excellence for Drug Discovery, Research Triangle Park, Durham, NC, USA
| | - Juan Manuel Domínguez
- GlaxoSmithKline R&D, Biological Reagents and Assay Development Department, Centro de Investigación Básica, Tres Cantos, Spain
| |
Collapse
|
18
|
Pasta S, Witkowski A, Joshi AK, Smith S. Catalytic Residues Are Shared between Two Pseudosubunits of the Dehydratase Domain of the Animal Fatty Acid Synthase. ACTA ACUST UNITED AC 2007; 14:1377-85. [DOI: 10.1016/j.chembiol.2007.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/31/2007] [Accepted: 11/05/2007] [Indexed: 10/22/2022]
|
19
|
Abstract
This review chronicles the synergistic growth of the fields of fatty acid and polyketide synthesis over the last century. In both animal fatty acid synthases and modular polyketide synthases, similar catalytic elements are covalently linked in the same order in megasynthases. Whereas in fatty acid synthases the basic elements of the design remain immutable, guaranteeing the faithful production of saturated fatty acids, in the modular polyketide synthases, the potential of the basic design has been exploited to the full for the elaboration of a wide range of secondary metabolites of extraordinary structural diversity.
Collapse
Affiliation(s)
- Stuart Smith
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA.
| | | |
Collapse
|
20
|
Richter CD, Stanmore DA, Miguel RN, Moncrieffe MC, Tran L, Brewerton S, Meersman F, Broadhurst RW, Weissman KJ. Autonomous folding of interdomain regions of a modular polyketide synthase. FEBS J 2007; 274:2196-209. [PMID: 17419733 DOI: 10.1111/j.1742-4658.2007.05757.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Domains within the multienzyme polyketide synthases are linked by noncatalytic sequences of variable length and unknown function. Recently, the crystal structure was reported of a portion of the linker between the acyltransferase (AT) and ketoreductase (KR) domains from module 1 of the erythromycin synthase (6-deoxyerythronolide B synthase), as a pseudodimer with the adjacent ketoreductase (KR). On the basis of this structure, the homologous linker region between the dehydratase (DH) and enoyl reductase (ER) domains in fully reducing modules has been proposed to occupy a position on the periphery of the polyketide synthases complex, as in porcine fatty acid synthase. We report here the expression and characterization of the same region of the 6-deoxyerythronolide B synthase module 1 AT-KR linker, without the adjacent KR domain (termed DeltaN AT1-KR1), as well as the corresponding section of the DH-ER linker. The linkers fold autonomously and are well structured. However, analytical gel filtration and ultracentrifugation analysis independently show that DeltaN AT1-KR1 is homodimeric in solution; site-directed mutagenesis further demonstrates that linker self-association is compatible with the formation of a linker-KR pseudodimer. Our data also strongly indicate that the DH-ER linker associates with the upstream DH domain. Both of these findings are incompatible with the proposed model for polyketide synthase architecture, suggesting that it is premature to allocate the linker regions to a position in the multienzymes based on the solved structure of animal fatty acid synthase.
Collapse
|
21
|
Witkowski A, Joshi AK, Smith S. Coupling of the de novo fatty acid biosynthesis and lipoylation pathways in mammalian mitochondria. J Biol Chem 2007; 282:14178-85. [PMID: 17374604 DOI: 10.1074/jbc.m701486200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The objective of this study was to identify the products and possible role of a putative pathway for de novo fatty acid synthesis in mammalian mitochondria. Bovine heart mitochondrial matrix preparations were prepared free from contamination by proteins from other subcellular components and, using a combination of radioisotopic labeling and mass spectrometry, were shown to contain all of the enzymes required for the extension of a 2-carbon precursor by malonyl moieties to saturated acyl-ACP thioesters containing up to 14 carbon atoms. A major product was octanoyl-ACP and, in the presence of the apo-H-protein of the glycine cleavage complex, the newly synthesized octanoyl moieties were translocated to the lipoylation site on the acceptor protein. These studies demonstrate that one of the functions of the de novo fatty acid biosynthetic pathway in mammalian mitochondria is to provide the octanoyl precursor required for the essential protein lipoylation pathway.
Collapse
Affiliation(s)
- Andrzej Witkowski
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | | |
Collapse
|
22
|
Cox RJ. Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem 2007; 5:2010-26. [PMID: 17581644 DOI: 10.1039/b704420h] [Citation(s) in RCA: 352] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungi produce a wide variety of biologically active compounds. Among these, the polyketides form a large and structurally diverse group. These compounds are synthesised by highly programmed and very large iterative multifunctional proteins, the polyketide synthases, with nm dimensions. This review outlines the current state of knowledge regarding the links between gene sequence, protein architecture and biosynthetic programming for fungal polyketide synthases.
Collapse
Affiliation(s)
- Russell J Cox
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK BS8 1TS.
| |
Collapse
|
23
|
Borgos SEF, Tsan P, Sletta H, Ellingsen TE, Lancelin JM, Zotchev SB. Probing the structure-function relationship of polyene macrolides: engineered biosynthesis of soluble nystatin analogues. J Med Chem 2006; 49:2431-9. [PMID: 16610786 DOI: 10.1021/jm050895w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although polyene macrolides are efficient antifungal agents with fungicidal mode of action, their use in medical practice is problematic due to their low solubility and significant human toxicity. In an attempt to address the solubility problem, we have obtained two analogues of nystatin with hydroxy groups at positions C31 and C33 through manipulation of the nystatin polyketide synthase in the producing organism Streptomyces noursei. Structures of the analogues were confirmed by nuclear magnetic resonance (NMR), and their solubility was found to be more than 2000 times higher than that of nystatin. However, both analogues were shown to have lost antifungal activity, implying that the integrity of the hydrophobic polyene region of the nystatin molecule is crucial for the fungicidal action. NMR data and computer modeling performed for the new analogues suggested conformational changes together with a significantly increased structural disorder, which may account for both increased solubility and the loss of activity.
Collapse
Affiliation(s)
- Sven E F Borgos
- Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | | | | | | | | | | |
Collapse
|
24
|
Keatinge-Clay AT, Stroud RM. The Structure of a Ketoreductase Determines the Organization of the β-Carbon Processing Enzymes of Modular Polyketide Synthases. Structure 2006; 14:737-48. [PMID: 16564177 DOI: 10.1016/j.str.2006.01.009] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 01/11/2006] [Accepted: 01/17/2006] [Indexed: 11/18/2022]
Abstract
The structure of the ketoreductase (KR) from the first module of the erythromycin synthase with NADPH bound was solved to 1.79 A resolution. The 51 kDa domain has two subdomains, each similar to a short-chain dehydrogenase/reductase (SDR) monomer. One subdomain has a truncated Rossmann fold and serves a purely structural role stabilizing the other subdomain, which catalyzes the reduction of the beta-carbonyl of a polyketide and possibly the epimerization of an alpha-substituent. The structure enabled us to define the domain boundaries of KR, the dehydratase (DH), and the enoylreductase (ER). It also constrains the three-dimensional organization of these domains within a module, revealing that KR does not make dimeric contacts across the 2-fold axis of the module. The quaternary structure elucidates how substrates are shuttled between the active sites of polyketide synthases (PKSs), as well as related fatty acid synthases (FASs), and suggests how domains can be swapped to make hybrid synthases that produce novel polyketides.
Collapse
Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16(th) Street, San Francisco, California 94107, USA.
| | | |
Collapse
|
25
|
Carlisle-Moore L, Gordon CR, Machutta CA, Miller WT, Tonge PJ. Substrate recognition by the human fatty-acid synthase. J Biol Chem 2005; 280:42612-8. [PMID: 16215233 PMCID: PMC2442872 DOI: 10.1074/jbc.m507082200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human fatty-acid synthase (HFAS) is a potential target for anti-tumor drug discovery. As a prelude to the design of compounds that target the enoyl reductase (ER) component of HFAS, the recognition of NADPH and exogenous substrates by the ER active site has been investigated. Previous studies demonstrate that modification of Lys-1699 by pyridoxal 5'-phosphate results in a specific decrease in ER activity. For the overall HFAS reaction, the K1699A and K1699Q mutations reduced kcat and kcat/KNADPH by 8- and 600-fold, respectively (where KNADPH indicates the Km value for NADPH). Thus, Lys-1699 contributes 4 kcal/mol to stabilization of the rate-limiting transition state following NADPH binding, while also stabilizing the most stable ground state after NADPH binding by 3 kcal/mol. A similar effect of the mutations on the ER partial reaction was observed, in agreement with the proposal that Lys-1699 is located in the ER NADPH-binding site. Most unexpectedly, however, both kcat and kcat/KNADPH for the beta-ketoacyl reductase (BKR) reaction were also impacted by the Lys-1699 mutations, raising the possibility that the ER and BKR activities share a single active site. However, based on previous data indicating that the two reductase activities utilize distinct cofactor binding sites, mutagenesis of Lys-1699 is hypothesized to modulate BKR activity via allosteric effects between the ER and BKR NADPH sites.
Collapse
Affiliation(s)
- Loretha Carlisle-Moore
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-3400
| | - Chris R. Gordon
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-3400
| | - Carl A. Machutta
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-3400
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-3400
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794-3400
- To whom correspondence should be addressed: Dept. of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400. Tel.: 631-632-7907; Fax: 631-632-7934; E-mail:
| |
Collapse
|
26
|
Asturias FJ, Chadick JZ, Cheung IK, Stark H, Witkowski A, Joshi AK, Smith S. Structure and molecular organization of mammalian fatty acid synthase. Nat Struct Mol Biol 2005; 12:225-32. [PMID: 15711565 DOI: 10.1038/nsmb899] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 01/19/2005] [Indexed: 11/09/2022]
Abstract
De novo synthesis of fatty acids in the cytosol of animal cells is carried out by the multifunctional, homodimeric fatty acid synthase (FAS). Cryo-EM analysis of single FAS particles imaged under conditions that limit conformational variability, combined with gold labeling of the N termini and structural analysis of the FAS monomers, reveals two coiled monomers in an overlapping arrangement. Comparison of dimeric FAS structures related to different steps in the fatty acid synthesis process indicates that only limited local rearrangements are required for catalytic interaction among different functional domains. Monomer coiling probably contributes to FAS efficiency and provides a structural explanation for the reported activity of a FAS monomer dimerized to a catalytically inactive partner. The new FAS structure provides a new paradigm for understanding the architecture of FAS and the related modular polyketide synthases.
Collapse
Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | | | | | | | | | | | | |
Collapse
|
27
|
Witkowski A, Ghosal A, Joshi AK, Witkowska HE, Asturias FJ, Smith S. Head-to-Head Coiled Arrangement of the Subunits of the Animal Fatty Acid Synthase. ACTA ACUST UNITED AC 2004; 11:1667-76. [PMID: 15610851 DOI: 10.1016/j.chembiol.2004.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 09/25/2004] [Accepted: 09/30/2004] [Indexed: 10/26/2022]
Abstract
The role of the beta-ketoacyl synthase domains in dimerization of the 2505 residue subunits of the multifunctional animal FAS has been evaluated by a combination of crosslinking and characterization of several truncated forms of the protein. Polypeptides containing only the N-terminal 971 residues can form dimers, but polypeptides lacking only the N-terminal 422 residue beta-ketoacyl synthase domain cannot. FAS subunits can be crosslinked with spacer lengths as short as 6 A, via cysteine residues engineered near the N terminus of the full-length polypeptides. The proximity of the N-terminal beta-ketoacyl synthase domains and their essential role in dimerization is consistent with a revised model for the FAS in which a head-to-head arrangement of two coiled subunits facilitates functional interactions between the dimeric beta-ketoacyl synthase and the acyl carrier protein domains of either subunit.
Collapse
Affiliation(s)
- Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA
| | | | | | | | | | | |
Collapse
|