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Zhou J, Zhang L, Wang Y, Song W, Huang Y, Mu Y, Schmitz W, Zhang SY, Lin H, Chen HZ, Ye F, Zhang L. The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202313109. [PMID: 37779101 DOI: 10.1002/anie.202313109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a "rheostat" α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.
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Affiliation(s)
- Jiashen Zhou
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiran Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Wenyan Song
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuzhou Huang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, 97074, Germany
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Fei Ye
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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2
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Ye S, Magadán-Corpas P, Pérez-Valero Á, Villar CJ, Lombó F. Metabolic engineering strategies for naringenin production enhancement in Streptomyces albidoflavus J1074. Microb Cell Fact 2023; 22:167. [PMID: 37644530 PMCID: PMC10466684 DOI: 10.1186/s12934-023-02172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Naringenin is an industrially relevant compound due to its multiple pharmaceutical properties as well as its central role in flavonoid biosynthesis. RESULTS On our way to develop Streptomyces albidoflavus J1074 as a microbial cell factory for naringenin production, we have significantly increased the yields of this flavanone by combining various metabolic engineering strategies, fermentation strategies and genome editing approaches in a stepwise manner. Specifically, we have screened different cultivation media to identify the optimal production conditions and have investigated how the additive feeding of naringenin precursors influences the production. Furthermore, we have employed genome editing strategies to remove biosynthetic gene clusters (BGCs) associated with pathways that might compete with naringenin biosynthesis for malonyl-CoA precursors. Moreover, we have expressed MatBC, coding for a malonate transporter and an enzyme responsible for the conversion of malonate into malonyl-CoA, respectively, and have duplicated the naringenin BGC, further contributing to the production improvement. By combining all of these strategies, we were able to achieve a remarkable 375-fold increase (from 0.06 mg/L to 22.47 mg/L) in naringenin titers. CONCLUSION This work demonstrates the influence that fermentation conditions have over the final yield of a bioactive compound of interest and highlights various bottlenecks that affect production. Once such bottlenecks are identified, different strategies can be applied to overcome them, although the efficiencies of such strategies may vary and are difficult to predict.
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Affiliation(s)
- Suhui Ye
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- Principality of Asturias, IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Patricia Magadán-Corpas
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- Principality of Asturias, IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Álvaro Pérez-Valero
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- Principality of Asturias, IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Claudio J Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- Principality of Asturias, IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.
- Principality of Asturias, IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Principality of Asturias, Spain.
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain.
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3
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Rohand T, Ben El Ayouchia H, Achtak H, Ghaleb A, Derin Y, Tutar A, Tanemura K. Design, synthesis, DFT calculations, molecular docking and antimicrobial activities of novel cobalt, chromium metal complexes of heterocyclic moiety-based 1,3,4-oxadiazole derivatives. J Biomol Struct Dyn 2022; 40:11837-11850. [PMID: 34402765 DOI: 10.1080/07391102.2021.1965031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A Schiff base, 5-(4-methylphenyl)-4-[(pyridin-2-ylmethylidene)amino]-4H-1,2,4-oxadiazole as a bidentate ligand has been synthesized by the reaction between the 4-amino-5-(4-methylphenyl)-4H-1,3,4-oxadiazole and aromatic aldehyde. The Schiff base reacted with CoCl3·6H2O and CrCl3·6H2O in ethanol to yield 1,3,4-oxadiazole complexes. The structures of synthesized ligand and their complexes have been established on the basis of their IR, Mass and 1H-NMR spectra. Electronic and geometric structures of both cobalt and chromium complexes were investigated by density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) calculations. DFT-based reactivity calculations estimated the studied system as strong electrophile and/or strong nucleophile in polar organic reactions. Moreover, most reactive sites were predicted theoretically based on the delocalized and localized indexes. The nature of Ligand-Metal chemical bonding is discussed in terms of the natural bond orbital (NBO) and QTAIM analysis. Accordingly, the metal ions such as cobalt and chromium are bidentate coordinated with the Schiff base by nitrogen atoms of imine function and pyridine, to form stable complexes. Furthermore, the chromium ions have an affinity superior to the cobalt ions towards Schiff base ligand. In addition, the results of the antibacterial activity in-vitro show that the metal complexation confers an increase in the antibacterial activity of the complexed ligand compared to the free ligand against both Gram-positive and Gram-negative bacteria with broad spectrum activity. In silico molecular docking studies of the ligands and their complexes were applied to describe the probable binding modes into the active site of Escherichia coli (E. coli) FabH and Salmonella typhimurium LT2 neuraminidase (STNA) receptors. The increase in biological activity could be attributed to the high stability of the complexes and strong affinities to bacterial enzyme receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taoufik Rohand
- Laboratoire de Chimie Analytique et Moléculaire, Département de Chimie, Université Cadi Ayyad, Faculté Polydisciplinaire Safi, Safi, Morocco
| | - Hicham Ben El Ayouchia
- Laboratoire de Chimie Analytique et Moléculaire, Département de Chimie, Université Cadi Ayyad, Faculté Polydisciplinaire Safi, Safi, Morocco
| | - Hafid Achtak
- Department of Biology, Environment and Health Research Team, Polydisciplinary Faculty, Cadi Ayyad University, Safi, Morocco
| | - Adib Ghaleb
- Laboratoire de Chimie Analytique et Moléculaire, Département de Chimie, Université Cadi Ayyad, Faculté Polydisciplinaire Safi, Safi, Morocco
| | - Yavuz Derin
- Department of Chemistry, Sakarya University, Sakarya, Turkey
| | - Ahmet Tutar
- Department of Chemistry, Sakarya University, Sakarya, Turkey
| | - Kiyoshi Tanemura
- Chemical Laboratory, School of Life Dentistry at Niigata, Nippon Dental University, Niigata, Japan
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4
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Siroli L, Braschi G, Rossi S, Gottardi D, Patrignani F, Lanciotti R. Lactobacillus paracasei A13 and High-Pressure Homogenization Stress Response. Microorganisms 2020; 8:E439. [PMID: 32244939 PMCID: PMC7143770 DOI: 10.3390/microorganisms8030439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/14/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
Sub-lethal high-pressure homogenization treatments applied to Lactobacillus paracasei A13 demonstrated to be a useful strategy to enhance technological and functional properties without detrimental effects on the viability of this strain. Modification of membrane fatty acid composition is reported to be the main regulatory mechanisms adopted by probiotic lactobacilli to counteract high-pressure stress. This work is aimed to clarify and understand the relationship between the modification of membrane fatty acid composition and the expression of genes involved in fatty acid biosynthesis in Lactobacillus paracasei A13, before and after the application of different sub-lethal hyperbaric treatments. Our results showed that Lactobacillus paracasei A13 activated a series of reactions aimed to control and stabilize membrane fluidity in response to high-pressure homogenization treatments. In fact, the production of cyclic fatty acids was counterbalanced by the unsaturation and elongation of fatty acids. The gene expression data indicate an up-regulation of the genes accA, accC, fabD, fabH and fabZ after high-pressure homogenization treatment at 150 and 200 MPa, and of fabK and fabZ after a treatment at 200 MPa suggesting this regulation of the genes involved in fatty acids biosynthesis as an immediate response mechanism adopted by Lactobacillus paracasei A13 to high-pressure homogenization treatments to balance the membrane fluidity. Although further studies should be performed to clarify the modulation of phospholipids and glycoproteins biosynthesis since they play a crucial role in the functional properties of the probiotic strains, this study represents an important step towards understanding the response mechanisms of Lactobacillus paracasei A13 to sub-lethal high-pressure homogenization treatments.
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Affiliation(s)
- Lorenzo Siroli
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Giacomo Braschi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Samantha Rossi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Davide Gottardi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
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5
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Patterson EI, Nanson JD, Abendroth J, Bryan C, Sankaran B, Myler PJ, Forwood JK. Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Proteins 2019; 88:47-56. [PMID: 31237717 DOI: 10.1002/prot.25765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/08/2022]
Abstract
The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.
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Affiliation(s)
- Edward I Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.,The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD, Australia
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,UCB Beryllium Discovery Corp, Bainbridge Island, Washington
| | - Cassie Bryan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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6
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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7
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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8
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Jensen MR, Goblirsch BR, Esler MA, Christenson JK, Mohamed FA, Wackett LP, Wilmot CM. The role of OleA His285 in orchestration of long-chain acyl-coenzyme A substrates. FEBS Lett 2018; 592:987-998. [PMID: 29430657 DOI: 10.1002/1873-3468.13004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/19/2018] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
Renewable production of hydrocarbons is being pursued as a petroleum-independent source of commodity chemicals and replacement for biofuels. The bacterial biosynthesis of long-chain olefins represents one such platform. The process is initiated by OleA catalyzing the condensation of two fatty acyl-coenzyme A substrates to form a β-keto acid. Here, the mechanistic role of the conserved His285 is investigated through mutagenesis, activity assays, and X-ray crystallography. Our data demonstrate that His285 is required for product formation, influences the thiolase nucleophile Cys143 and the acyl-enzyme intermediate before and after transesterification, and orchestrates substrate coordination as a defining component of an oxyanion hole. As a consequence, His285 plays a key role in enabling a mechanistic strategy in OleA that is distinct from other thiolases.
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Affiliation(s)
- Matthew R Jensen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.,The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Brandon R Goblirsch
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Morgan A Esler
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.,The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - James K Christenson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.,The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Fatuma A Mohamed
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.,The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Carrie M Wilmot
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, MN, USA.,The BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
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9
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Robbins T, Kapilivsky J, Cane DE, Khosla C. Roles of Conserved Active Site Residues in the Ketosynthase Domain of an Assembly Line Polyketide Synthase. Biochemistry 2016; 55:4476-84. [PMID: 27441852 DOI: 10.1021/acs.biochem.6b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ketosynthase (KS) domains of assembly line polyketide synthases (PKSs) catalyze intermodular translocation of the growing polyketide chain as well as chain elongation via decarboxylative Claisen condensation. The mechanistic roles of ten conserved residues in the KS domain of Module 1 of the 6-deoxyerythronolide B synthase were interrogated via site-directed mutagenesis and extensive biochemical analysis. Although the C211A mutant at the KS active site exhibited no turnover activity, it was still a competent methylmalonyl-ACP decarboxylase. The H346A mutant exhibited reduced rates of both chain translocation and chain elongation, with a greater effect on the latter half-reaction. H384 contributed to methylmalonyl-ACP decarboxylation, whereas K379 promoted C-C bond formation. S315 played a role in coupling decarboxylation to C-C bond formation. These findings support a mechanism for the translocation and elongation half-reactions that provides a well-defined starting point for further analysis of the key chain-building domain in assembly line PKSs.
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Affiliation(s)
- Thomas Robbins
- Departments of Chemistry and Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - Joshuah Kapilivsky
- Departments of Chemistry and Chemical Engineering, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemistry and Chemical Engineering, Stanford University , Stanford, California 94305, United States
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10
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Schaefer CM, Lu R, Nesbitt NM, Schiebel J, Sampson NS, Kisker C. FadA5 a thiolase from Mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. Structure 2014; 23:21-33. [PMID: 25482540 DOI: 10.1016/j.str.2014.10.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/18/2014] [Accepted: 10/06/2014] [Indexed: 11/29/2022]
Abstract
With the exception of HIV, tuberculosis (TB) is the leading cause of mortality among infectious diseases. The urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant Mycobacterium tuberculosis (Mtb) strains. Proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against TB. FadA5, a thiolase from Mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation under release of critical metabolites and was shown to be of importance during the chronic stage of TB infections. To gain structural and mechanistic insight on FadA5, we characterized the enzyme in different stages of the cleavage reaction and with a steroid bound to the binding pocket. Structural comparisons to human thiolases revealed that it should be possible to target FadA5 specifically, and the steroid-bound structure provides a solid basis for the development of inhibitors against FadA5.
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Affiliation(s)
- Christin M Schaefer
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Rui Lu
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Natasha M Nesbitt
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.
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11
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Zheng Z, Parsons JB, Tangallapally R, Zhang W, Rock CO, Lee RE. Discovery of novel bacterial elongation condensing enzyme inhibitors by virtual screening. Bioorg Med Chem Lett 2014; 24:2585-8. [PMID: 24755430 PMCID: PMC4425204 DOI: 10.1016/j.bmcl.2014.03.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/07/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
The elongation condensing enzymes in the bacterial fatty acid biosynthesis pathway represent desirable targets for the design of novel, broad-spectrum antimicrobial agents. A series of substituted benzoxazolinones was identified in this study as a novel class of elongation condensing enzyme (FabB and FabF) inhibitors using a two-step virtual screening approach. Structure activity relationships were developed around the benzoxazolinone scaffold showing that N-substituted benzoxazolinones were most active. The benzoxazolinone scaffold has high chemical tractability making this chemotype suitable for further development of bacterial fatty acid synthesis inhibitors.
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Affiliation(s)
- Zhong Zheng
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joshua B Parsons
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Weixing Zhang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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12
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Trajtenberg F, Altabe S, Larrieux N, Ficarra F, de Mendoza D, Buschiazzo A, Schujman GE. Structural insights into bacterial resistance to cerulenin. FEBS J 2014; 281:2324-38. [DOI: 10.1111/febs.12785] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/10/2014] [Accepted: 03/13/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Felipe Trajtenberg
- Institut Pasteur de Montevideo; Unit of Protein Crystallography; Montevideo Uruguay
| | - Silvia Altabe
- Instituto de Biología Molecular y Celular de Rosario (IBR) - CONICET; Facultad de Cs Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Argentina
| | - Nicole Larrieux
- Institut Pasteur de Montevideo; Unit of Protein Crystallography; Montevideo Uruguay
| | - Florencia Ficarra
- Instituto de Biología Molecular y Celular de Rosario (IBR) - CONICET; Facultad de Cs Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR) - CONICET; Facultad de Cs Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Argentina
| | - Alejandro Buschiazzo
- Institut Pasteur de Montevideo; Unit of Protein Crystallography; Montevideo Uruguay
- Département de Biologie Structurale et Chimie; Institut Pasteur; Paris France
| | - Gustavo E. Schujman
- Instituto de Biología Molecular y Celular de Rosario (IBR) - CONICET; Facultad de Cs Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Argentina
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13
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Lee W, Engels B. The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate. Biochemistry 2014; 53:919-31. [DOI: 10.1021/bi401308j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wook Lee
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
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14
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Schiebel J, Kapilashrami K, Fekete A, Bommineni GR, Schaefer CM, Mueller MJ, Tonge PJ, Kisker C. Structural basis for the recognition of mycolic acid precursors by KasA, a condensing enzyme and drug target from Mycobacterium tuberculosis. J Biol Chem 2013; 288:34190-34204. [PMID: 24108128 DOI: 10.1074/jbc.m113.511436] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The survival of Mycobacterium tuberculosis depends on mycolic acids, very long α-alkyl-β-hydroxy fatty acids comprising 60-90 carbon atoms. However, despite considerable efforts, little is known about how enzymes involved in mycolic acid biosynthesis recognize and bind their hydrophobic fatty acyl substrates. The condensing enzyme KasA is pivotal for the synthesis of very long (C38-42) fatty acids, the precursors of mycolic acids. To probe the mechanism of substrate and inhibitor recognition by KasA, we determined the structure of this protein in complex with a mycobacterial phospholipid and with several thiolactomycin derivatives that were designed as substrate analogs. Our structures provide consecutive snapshots along the reaction coordinate for the enzyme-catalyzed reaction and support an induced fit mechanism in which a wide cavity is established through the concerted opening of three gatekeeping residues and several α-helices. The stepwise characterization of the binding process provides mechanistic insights into the induced fit recognition in this system and serves as an excellent foundation for the development of high affinity KasA inhibitors.
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Affiliation(s)
- Johannes Schiebel
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany; Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Kanishk Kapilashrami
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Agnes Fekete
- Julius-von-Sachs Institute of Biosciences, Biocenter, Department of Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Gopal R Bommineni
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Christin M Schaefer
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Martin J Mueller
- Julius-von-Sachs Institute of Biosciences, Biocenter, Department of Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Peter J Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany.
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15
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Lee W, Engels B. Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State. J Phys Chem B 2013; 117:8095-104. [DOI: 10.1021/jp403067m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wook Lee
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
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16
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Xu W, Qiao K, Tang Y. Structural analysis of protein-protein interactions in type I polyketide synthases. Crit Rev Biochem Mol Biol 2012; 48:98-122. [PMID: 23249187 DOI: 10.3109/10409238.2012.745476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Polyketide synthases (PKSs) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. The PKSs consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. Biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. Recent developments on X-ray crystallography and protein NMR techniques have allowed us to understand the biosynthetic mechanism of these enzymes from their structures. These structural studies have facilitated the elucidation of the sequence-function relationship of PKSs and will ultimately contribute to the prediction of product structure. This review will focus on the current knowledge of type I PKS structures and the protein-protein interactions in this system.
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Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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17
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Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
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18
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Lee W, Luckner SR, Kisker C, Tonge PJ, Engels B. Elucidation of the protonation states of the catalytic residues in mtKasA: implications for inhibitor design. Biochemistry 2011; 50:5743-56. [PMID: 21615093 DOI: 10.1021/bi200006t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
KasA (β-ketoacyl ACP synthase I) is involved in the biosynthetic pathway of mycolic acids, an essential component of the cell wall in Mycobacterium tuberculosis. It was shown that KasA is essential for the survival of the pathogen and thus could serve as a new drug target for the treatment of tuberculosis. The active site of KasA was previously characterized by X-ray crystallography. However, questions regarding the protonation state of specific amino acids, the orientation of the histidine groups within the active site, and additional conformers being accessible at ambient temperatures remain open and have to be addressed prior to the design of new inhibitors. We investigate the active site of KasA in this work by means of structural motifs and relative energies. Molecular dynamics (MD) simulations, free energy perturbation computations, and calculations employing the hybrid quantum mechanics/molecular mechanics (QM/MM) method made it possible to determine the protonation status and reveal important details about the catalytic mechanism of KasA. Additionally, we can rationalize the molecular basis for the acyl-transfer activity in the H311A mutant. Our data strongly suggest that inhibitors should be able to inhibit different protonation states because the enzyme can switch easily between a zwitterionic and neutral state.
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Affiliation(s)
- Wook Lee
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97070 Würzburg, Germany
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19
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Ramelot TA, Smola MJ, Lee HW, Ciccosanti C, Hamilton K, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Kennedy MA. Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis. Biochemistry 2011; 50:1442-53. [PMID: 21235239 PMCID: PMC3063093 DOI: 10.1021/bi101932s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GmACP3 from Geobacter metallireducens is a specialized acyl carrier protein (ACP) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (LPS) biosynthesis, indicating a likely function for GmACP3 in LPS production. By overexpression in Escherichia coli, about 50% holo-GmACP3 and 50% apo-GmACP3 were obtained. Apo-GmACP3 exhibited slow precipitation and non-monomeric behavior by (15)N NMR relaxation measurements. Addition of 4'-phosphopantetheine (4'-PP) via enzymatic conversion by E. coli holo-ACP synthase resulted in stable >95% holo-GmACP3 that was characterized as monomeric by (15)N relaxation measurements and had no indication of conformational exchange. We have determined a high-resolution solution structure of holo-GmACP3 by standard NMR methods, including refinement with two sets of NH residual dipolar couplings, allowing for a detailed structural analysis of the interactions between 4'-PP and GmACP3. Whereas the overall four helix bundle topology is similar to previously solved ACP structures, this structure has unique characteristics, including an ordered 4'-PP conformation that places the thiol at the entrance to a central hydrophobic cavity near a conserved hydrogen-bonded Trp-His pair. These residues are part of a conserved WDSLxH/N motif found in GmACP3 and its orthologs. The helix locations and the large hydrophobic cavity are more similar to medium- and long-chain acyl-ACPs than to other apo- and holo-ACP structures. Taken together, structural characterization along with bioinformatic analysis of nearby genes suggests that GmACP3 is involved in lipid A acylation, possibly by atypical long-chain hydroxy fatty acids, and potentially is involved in synthesis of secondary metabolites.
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Affiliation(s)
- Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Matthew J. Smola
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Colleen Ciccosanti
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Keith Hamilton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - John K. Everett
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, 08854, United States
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
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20
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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.
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21
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Bagautdinov B, Ukita Y, Miyano M, Kunishima N. Structure of 3-oxoacyl-(acyl-carrier protein) synthase II from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:358-66. [PMID: 18453702 PMCID: PMC2376401 DOI: 10.1107/s1744309108010336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 04/15/2008] [Indexed: 11/10/2022]
Abstract
The beta-ketoacyl-(acyl carrier protein) synthases (beta-keto-ACP synthases; KAS) catalyse the addition of two-carbon units to the growing acyl chain during the elongation phase of fatty-acid synthesis. As key regulators of bacterial fatty-acid synthesis, they are promising targets for the development of new antibacterial agents. The crystal structure of 3-oxoacyl-ACP synthase II from Thermus thermophilus HB8 (TtKAS II) has been solved by molecular replacement and refined at 2.0 A resolution. The crystal is orthorhombic, space group P2(1)2(1)2, with unit-cell parameters a = 72.07, b = 185.57, c = 62.52 A, and contains one homodimer in the asymmetric unit. The subunits adopt the well known alpha-beta-alpha-beta-alpha thiolase fold that is common to ACP synthases. The structural and sequence similarities of TtKAS II to KAS I and KAS II enzymes of known structure from other sources support the hypothesis of comparable enzymatic activity. The dimeric state of TtKAS II is important to create each fatty-acid-binding pocket. Closer examination of KAS structures reveals that compared with other KAS structures in the apo form, the active site of TtKAS II is more accessible because of the ;open' conformation of the Phe396 side chain.
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Affiliation(s)
- Bagautdin Bagautdinov
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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22
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Schujman GE, Altabe S, de Mendoza D. A malonyl-CoA-dependent switch in the bacterial response to a dysfunction of lipid metabolism. Mol Microbiol 2008; 68:987-96. [PMID: 18384517 DOI: 10.1111/j.1365-2958.2008.06202.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria stringently regulate the synthesis of their membrane phospholipids, but the responsible regulatory mechanisms are incompletely understood. Bacillus subtilis FabF, the target of the mycotoxin cerulenin, catalyses the condensation of malonyl-ACP with acyl-ACP to extend the growing acyl chain by two carbons. Here we show that B. subtilis strains containing the fabF1 allele, which codes for the cerulenin-insensitive protein FabF[I108F], overexpressed several genes involved in fatty acid and phospholipid biosynthesis (the fap regulon) and had significantly elevated levels of malonyl-CoA. These results pinpointed FabF[I108F] as responsible for the increased malonyl-CoA production, which in turn acts as an inducer of the fap regulon by impairing the binding of the FapR repressor to its DNA targets. Synthesis of acyl-ACPs by a cell-free fatty acid system prepared from fabF1 cells showed the accumulation of short- and medium-chain acyl-ACPs. These results indicate that the acyl-ACP chain length acceptance of FabF[I108F] is biased towards shorter acyl-ACPs. We also provide evidence that upregulation of FabF[I108F] is essential for survival and for resistance to cerulenin of fabF1 cells. These findings indicate that malonyl-CoA is a key molecule to monitor lipid metabolism functioning and trigger appropriate genetic and biochemical adjustments to relieve dysfunctions of this essential metabolic pathway.
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Affiliation(s)
- Gustavo E Schujman
- Instituto de Biología Molecular y Celular de Rosario, and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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23
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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.
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Affiliation(s)
- Stuart Smith
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA.
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24
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Christensen CE, Kragelund BB, von Wettstein-Knowles P, Henriksen A. Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase. Protein Sci 2007; 16:261-72. [PMID: 17242430 PMCID: PMC2203288 DOI: 10.1110/ps.062473707] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Two distinct ways of organizing fatty acid biosynthesis exist: the multifunctional type I fatty acid synthase (FAS) of mammals, fungi, and lower eukaryotes with activities residing on one or two polypeptides; and the dissociated type II FAS of prokaryotes, plastids, and mitochondria with individual activities encoded by discrete genes. The beta-ketoacyl [ACP] synthase (KAS) moiety of the mitochondrial FAS (mtKAS) is targeted by the antibiotic cerulenin and possibly by the other antibiotics inhibiting prokaryotic KASes: thiolactomycin, platensimycin, and the alpha-methylene butyrolactone, C75. The high degree of structural similarity between mitochondrial and prokaryotic KASes complicates development of novel antibiotics targeting prokaryotic KAS without affecting KAS domains of cytoplasmic FAS. KASes catalyze the C(2) fatty acid elongation reaction using either a Cys-His-His or Cys-His-Asn catalytic triad. Three KASes with different substrate specificities participate in synthesis of the C(16) and C(18) products of prokaryotic FAS. By comparison, mtKAS carries out all elongation reactions in the mitochondria. We present the X-ray crystal structures of the Cys-His-His-containing human mtKAS and its hexanoyl complex plus the hexanoyl complex of the plant mtKAS from Arabidopsis thaliana. The structures explain (1) the bimodal (C(6) and C(10)-C(12)) substrate preferences leading to the C(8) lipoic acid precursor and long chains for the membranes, respectively, and (2) the low cerulenin sensitivity of the human enzyme; and (3) reveal two different potential acyl-binding-pocket extensions. Rearrangements taking place in the active site, including subtle changes in the water network, indicate a change in cooperativity of the active-site histidines upon primer binding.
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25
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Sridharan S, Wang L, Brown AK, Dover LG, Kremer L, Besra GS, Sacchettini JC. X-ray crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase II (mtKasB). J Mol Biol 2007; 366:469-80. [PMID: 17174327 PMCID: PMC2590929 DOI: 10.1016/j.jmb.2006.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 10/27/2006] [Accepted: 11/02/2006] [Indexed: 01/07/2023]
Abstract
Mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the Mycobacterium tuberculosis cell wall. Through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. Mycobacteria possess two fatty acid synthases (FAS); FAS-I carries out de novo synthesis of fatty acids while FAS-II is considered to elongate medium chain length fatty acyl primers to provide long chain (C(56)) precursors of mycolic acids. Here we report the crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase (ACP) II mtKasB, a mycobacterial elongation condensing enzyme involved in FAS-II. This enzyme, along with the M. tuberculosis beta-ketoacyl ACP synthase I mtKasA, catalyzes the Claisen-type condensation reaction responsible for fatty acyl elongation in FAS-II and are potential targets for development of novel anti-tubercular drugs. The crystal structure refined to 2.4 A resolution revealed that, like other KAS-II enzymes, mtKasB adopts a thiolase fold but contains unique structural features in the capping region that may be crucial to its preference for longer fatty acyl chains than its counterparts from other bacteria. Modeling of mtKasA using the mtKasB structure as a template predicts the overall structures to be almost identical, but a larger entrance to the active site tunnel is envisaged that might contribute to the greater sensitivity of mtKasA to the inhibitor thiolactomycin (TLM). Modeling of TLM binding in mtKasB shows that the drug fits the active site poorly and results of enzyme inhibition assays using TLM analogues are wholly consistent with our structural observations. Consequently, the structure described here further highlights the potential of TLM as an anti-tubercular lead compound and will aid further exploration of the TLM scaffold towards the design of novel compounds, which inhibit mycobacterial KAS enzymes more effectively.
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Affiliation(s)
- Sudharsan Sridharan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Lei Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Alistair K. Brown
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lynn G. Dover
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Laurent Kremer
- Université Montpellier II, Case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
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26
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Zhang YM, Hurlbert J, White SW, Rock CO. Roles of the Active Site Water, Histidine 303, and Phenylalanine 396 in the Catalytic Mechanism of the Elongation Condensing Enzyme of Streptococcus pneumoniae. J Biol Chem 2006; 281:17390-17399. [PMID: 16618705 DOI: 10.1074/jbc.m513199200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
beta-Ketoacyl-ACP synthases catalyze the condensation steps in fatty acid and polyketide synthesis and are targets for the development of novel antibiotics and anti-obesity and anti-cancer agents. The roles of the active site residues in Streptococcus pneumoniae FabF (beta-ketoacyl-ACP synthase II; SpFabF) were investigated to clarify the mechanism for this enzyme superfamily. The nucleophilic cysteine of the active site triad was required for acyl-enzyme formation and the overall condensation activity. The two active site histidines in the elongation condensing enzyme have different electronic states and functions. His337 is essential for condensation activity, and its protonated Nepsilon stabilizes the negative charge developed on the malonyl thioester carbonyl in the transition state. The Nepsilon of His303 accelerated catalysis by deprotonating a structured active site water for nucleophilic attack on the C3 of malonate, releasing bicarbonate. Lys332 controls the electronic state of His303 and also plays a critical role in the positioning of His337. Phe396 functions as a gatekeeper that controls the order of substrate addition. These data assign specific roles for each active site residue and lead to a revised general mechanism for this important class of enzymes.
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Affiliation(s)
- Yong-Mei Zhang
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Jason Hurlbert
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Stephen W White
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles O Rock
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.
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von Wettstein-Knowles P, Olsen JG, McGuire KA, Henriksen A. Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases. FEBS J 2006; 273:695-710. [PMID: 16441657 DOI: 10.1111/j.1742-4658.2005.05101.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Beta-ketoacyl-acyl carrier protein (ACP) synthase enzymes join short carbon units to construct fatty acyl chains by a three-step Claisen condensation reaction. The reaction starts with a trans thioesterification of the acyl primer substrate from ACP to the enzyme. Subsequently, the donor substrate malonyl-ACP is decarboxylated to form a carbanion intermediate, which in the third step attacks C1 of the primer substrate giving rise to an elongated acyl chain. A subgroup of beta-ketoacyl-ACP synthases, including mitochondrial beta-ketoacyl-ACP synthase, bacterial plus plastid beta-ketoacyl-ACP synthases I and II, and a domain of human fatty acid synthase, have a Cys-His-His triad and also a completely conserved Lys in the active site. To examine the role of these residues in catalysis, H298Q, H298E and six K328 mutants of Escherichia colibeta-ketoacyl-ACP synthase I were constructed and their ability to carry out the trans thioesterification, decarboxylation and/or condensation steps of the reaction was ascertained. The crystal structures of wild-type and eight mutant enzymes with and/or without bound substrate were determined. The H298E enzyme shows residual decarboxylase activity in the pH range 6-8, whereas the H298Q enzyme appears to be completely decarboxylation deficient, showing that H298 serves as a catalytic base in the decarboxylation step. Lys328 has a dual role in catalysis: its charge influences acyl transfer to the active site Cys, and the steric restraint imposed on H333 is of critical importance for decarboxylation activity. This restraint makes H333 an obligate hydrogen bond donor at Nepsilon, directed only towards the active site and malonyl-ACP binding area in the fatty acid complex.
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29
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Schmid MB. Crystallizing new approaches for antimicrobial drug discovery. Biochem Pharmacol 2006; 71:1048-56. [PMID: 16458857 DOI: 10.1016/j.bcp.2005.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 12/07/2005] [Accepted: 12/09/2005] [Indexed: 11/29/2022]
Abstract
Over the past decade, the sequences of microbial genomes have accumulated, changing the strategies for the discovery of novel anti-infective agents. Targets have become plentiful, yet new antimicrobial agents have been slow to emerge from this effort. In part, this reflects the long discovery and development times needed to bring new drugs to market. In addition, bottlenecks have been revealed in the antimicrobial drug discovery process at the steps of identifying good leads, and optimizing those leads into drug candidates. The fruit of structural genomics may provide opportunities to overcome these bottlenecks and fill the antimicrobial pipeline, by using the tools of structure guided drug discovery (SGDD).
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Affiliation(s)
- Molly B Schmid
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
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30
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Haapalainen AM, Meriläinen G, Wierenga RK. The thiolase superfamily: condensing enzymes with diverse reaction specificities. Trends Biochem Sci 2006; 31:64-71. [PMID: 16356722 DOI: 10.1016/j.tibs.2005.11.011] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 10/25/2005] [Accepted: 11/25/2005] [Indexed: 11/22/2022]
Abstract
The formation of a carbon-carbon bond is an essential step in the biosynthetic pathways by which fatty acids and polyketides are made. The thiolase superfamily enzymes catalyse this carbon-carbon-bond formation via a thioester-dependent Claisen-condensation-reaction mechanism. In this way, fatty-acid chains and polyketides are made by sequentially adding simple building blocks, such as acetate units, to the growing molecule. A common feature of these enzymes is a reactive cysteine residue that is transiently acylated in the catalytic cycle. The wide catalytic diversity of the thiolase superfamily enzymes is of great interest. In particular, the type-III polyketide synthases make complicated compounds of great biological importance using multiple, subsequent condensation reactions, which are all catalysed in the same active-site cavity. The crucial metabolic importance of the bacterial fatty-acid-synthesizing enzymes stimulates in-depth studies that aim to develop efficient anti-bacterial drugs.
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Affiliation(s)
- Antti M Haapalainen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, PO Box 3000, FIN-90014, Finland
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31
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Abstract
The type II fatty acid synthetic pathway is the principal route for the production of membrane phospholipid acyl chains in bacteria and plants. The reaction sequence is carried out by a series of individual soluble proteins that are each encoded by a discrete gene, and the pathway intermediates are shuttled between the enzymes as thioesters of an acyl carrier protein. The Escherichia coli system is the paradigm for the study of this system, and high-resolution X-ray and/or NMR structures of representative members of every enzyme in the type II pathway are now available. The structural biology of these proteins reveals the specific three-dimensional features of the enzymes that explain substrate recognition, chain length specificity, and the catalytic mechanisms that define their roles in producing the multitude of products generated by the type II system. These structures are also a valuable resource to guide antibacterial drug discovery.
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Affiliation(s)
- Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
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Olsen JG, Rasmussen AV, von Wettstein-Knowles P, Henriksen A. Structure of the mitochondrial beta-ketoacyl-[acyl carrier protein] synthase from Arabidopsis and its role in fatty acid synthesis. FEBS Lett 2005; 577:170-4. [PMID: 15527780 DOI: 10.1016/j.febslet.2004.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 09/24/2004] [Accepted: 10/01/2004] [Indexed: 11/21/2022]
Abstract
Mitochondrial fatty acid synthesis is catalyzed by a dissociated fatty acid synthase similar to those of plant plastids and bacteria. The crystal structure of a mitochondrial beta-ketoacyl-[acyl carrier protein] synthase (mtKAS), namely that from Arabidopsis thaliana, has been determined for the first time. This enzyme accomplishes the vital condensation steps in constructing fatty acid carbon skeletons. The product profile of mtKAS is unusual in that C8 and C(14-16) fatty acyl chains predominate. An enzyme architecture that likely is the basis for the observed bimodal profile of mtKAS products can be derived from the shape of the acyl binding pocket.
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Affiliation(s)
- Johan G Olsen
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
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Zhang L, Joshi AK, Hofmann J, Schweizer E, Smith S. Cloning, expression, and characterization of the human mitochondrial beta-ketoacyl synthase. Complementation of the yeast CEM1 knock-out strain. J Biol Chem 2005; 280:12422-9. [PMID: 15668256 DOI: 10.1074/jbc.m413686200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A human beta-ketoacyl synthase implicated in a mitochondrial pathway for fatty acid synthesis has been identified, cloned, expressed, and characterized. Sequence analysis indicates that the protein is more closely related to freestanding counterparts found in prokaryotes and chloroplasts than it is to the beta-ketoacyl synthase domain of the human cytosolic fatty acid synthase. The full-length nuclear-encoded 459-residue protein includes an N-terminal sequence element of approximately 38 residues that functions as a mitochondrial targeting sequence. The enzyme can elongate acyl-chains containing 2-14 carbon atoms with malonyl moieties attached in thioester linkage to the human mitochondrial acyl carrier protein and is able to restore growth to the respiratory-deficient yeast mutant cem1 that lacks the endogenous mitochondrial beta-ketoacyl synthase and exhibits lowered lipoic acid levels. To date, four components of a putative type II mitochondrial fatty acid synthase pathway have been identified in humans: acyl carrier protein, malonyl transferase, beta-ketoacyl synthase, and enoyl reductase. The substrate specificity and complementation data for the beta-ketoacyl synthase suggest that, as in plants and fungi, in humans this pathway may play an important role in the generation of octanoyl-acyl carrier protein, the lipoic acid precursor, as well as longer chain fatty acids that are required for optimal mitochondrial function.
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Affiliation(s)
- Lei Zhang
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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Musayev F, Sachdeva S, Scarsdale JN, Reynolds KA, Wright HT. Crystal structure of a substrate complex of Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III (FabH) with lauroyl-coenzyme A. J Mol Biol 2005; 346:1313-21. [PMID: 15713483 DOI: 10.1016/j.jmb.2004.12.044] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 12/15/2004] [Accepted: 12/19/2004] [Indexed: 11/27/2022]
Abstract
Beta-ketoacyl-acyl carrier protein synthase III (FabH) catalyzes a two step reaction that initiates the pathway of fatty acid biosynthesis in plants and bacteria. In Mycobacterium tuberculosis, FabH catalyzes extension of lauroyl, myristoyl and palmitoyl groups from which cell wall mycolic acids of the bacterium are formed. The first step of the reaction is an acyl group transfer from acyl-coenzyme A to the active-site cysteine of the enzyme; the second step is acyl chain extension by two carbon atoms through Claisen condensation with malonyl-acyl carrier protein. We have previously determined the crystal structure of a type II, dissociated M.tuberculosis FabH, which catalyzes extension of lauroyl, myristoyl and palmitoyl groups. Here we describe the first long-chain Michaelis substrate complex of a FabH, that of lauroyl-coenzyme A with a catalytically disabled Cys-->Ala mutant of M.tuberculosis FabH. An elongated channel extending from the mutated active-site cysteine defines the acyl group binding locus that confers unique acyl substrate specificity on M.tuberculosis FabH. CoA lies in a second channel, bound primarily through interactions of its nucleotide group at the enzyme surface. The apparent weak association of CoA in this complex may play a role in the binding and dissociation of long chain acyl-CoA substrates and products and poses questions pertinent to the mechanism of this enzyme.
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Affiliation(s)
- Faik Musayev
- Institute of Structural Biology and Drug Discovery, Department of Medicinal Chemistry, Virginia Commonwealth University, 800 E. Leigh St., Suite 212, Richmond, VA 23219, USA
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Kursula P, Sikkilä H, Fukao T, Kondo N, Wierenga RK. High resolution crystal structures of human cytosolic thiolase (CT): a comparison of the active sites of human CT, bacterial thiolase, and bacterial KAS I. J Mol Biol 2005; 347:189-201. [PMID: 15733928 DOI: 10.1016/j.jmb.2005.01.018] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 01/05/2005] [Accepted: 01/06/2005] [Indexed: 10/25/2022]
Abstract
Thiolases belong to a superfamily of condensing enzymes that includes also beta-ketoacyl acyl carrier protein synthases (KAS enzymes), involved in fatty acid synthesis. Here, we describe the high resolution structure of human cytosolic acetoacetyl-CoA thiolase (CT), both unliganded (at 2.3 angstroms resolution) and in complex with CoA (at 1.6 angstroms resolution). CT catalyses the condensation of two molecules of acetyl-CoA to acetoacetyl-CoA, which is the first reaction of the metabolic pathway leading to the synthesis of cholesterol. CT is a homotetramer of exact 222 symmetry. There is an excess of positively charged residues at the interdimer surface leading towards the CoA-binding pocket, possibly important for the efficient capture of substrates. The geometry of the catalytic site, including the three catalytic residues Cys92, His 353, Cys383, and the two oxyanion holes, is highly conserved between the human and bacterial Zoogloea ramigera thiolase. In human CT, the first oxyanion hole is formed by Wat38 (stabilised by Asn321) and NE2(His353), and the second by N(Cys92) and N(Gly385). The active site of this superfamily is constructed on top of four active site loops, near Cys92, Asn321, His353, and Cys383, respectively. These loops were used for the superpositioning of CT on the bacterial thiolase and on the Escherichia coli KAS I. This comparison indicates that the two thiolase oxyanion holes also exist in KAS I at topologically equivalent positions. Interestingly, the hydrogen bonding interactions at the first oxyanion hole are different in thiolase and KAS I. In KAS I, the hydrogen bonding partners are two histidine NE2 atoms, instead of a water and a NE2 side-chain atom in thiolase. The second oxyanion hole is in both structures shaped by corresponding main chain peptide NH-groups. The possible importance of bound water molecules at the catalytic site of thiolase for the reaction mechanism is discussed.
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Affiliation(s)
- Petri Kursula
- Department of Biochemistry and Biocenter Oulu, P.O. Box 3000, FIN-90014 University of Oulu, Oulu, Finland
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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.
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Affiliation(s)
- Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA
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37
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Kimber MS, Martin F, Lu Y, Houston S, Vedadi M, Dharamsi A, Fiebig KM, Schmid M, Rock CO. The Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Pseudomonas aeruginosa. J Biol Chem 2004; 279:52593-602. [PMID: 15371447 DOI: 10.1074/jbc.m408105200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type II fatty acid biosynthesis systems are essential for membrane formation in bacteria, making the constituent proteins of this pathway attractive targets for antibacterial drug discovery. The third step in the elongation cycle of the type II fatty acid biosynthesis is catalyzed by beta-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase. There are two isoforms. FabZ, which catalyzes the dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP, is a universally expressed component of the bacterial type II system. FabA, the second isoform, as has more limited distribution in nature and, in addition to dehydration, also carries out the isomerization of trans-2- to cis-3-decenoyl-ACP as an essential step in unsaturated fatty acid biosynthesis. We report the structure of FabZ from the important human pathogen Pseudomonas aeruginosa at 2.5 A of resolution. PaFabZ is a hexamer (trimer of dimers) with the His/Glu catalytic dyad located within a deep, narrow tunnel formed at the dimer interface. Site-directed mutagenesis experiments showed that the obvious differences in the active site residues that distinguish the FabA and FabZ subfamilies of dehydratases do not account for the unique ability of FabA to catalyze isomerization. Because the catalytic machinery of the two enzymes is practically indistinguishable, the structural differences observed in the shape of the substrate binding channels of FabA and FabZ lead us to hypothesize that the different shapes of the tunnels control the conformation and positioning of the bound substrate, allowing FabA, but not FabZ, to catalyze the isomerization reaction.
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Wang H, Cronan JE. Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues. J Biol Chem 2004; 279:34489-95. [PMID: 15194690 DOI: 10.1074/jbc.m403874200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The anaerobic unsaturated fatty acid synthetic pathway of Escherichia coli requires two specialized proteins, FabA and FabB. However, the fabA and fabB genes are found only in the Gram-negative alpha- and gamma-proteobacteria, and thus other anaerobic bacteria must synthesize these acids using different enzymes. We report that the Gram-positive bacterium Enterococcus faecalis encodes a protein, annotated as FabZ1, that functionally replaces the E. coli FabA protein, although the sequence of this protein aligns much more closely with E. coli FabZ, a protein that plays no specific role in unsaturated fatty acid synthesis. Therefore E. faecalis FabZ1 is a bifunctional dehydratase/isomerase, an enzyme activity heretofore confined to a group of Gram-negative bacteria. The FabZ2 protein is unable to replace the function of E. coli FabZ, although FabZ2, a second E. faecalis FabZ homologue, has this ability. Moreover, an E. faecalis FabF homologue (FabF1) was found to replace the function of E. coli FabB, whereas a second FabF homologue was inactive. From these data it is clear that bacterial fatty acid biosynthetic pathways cannot be deduced solely by sequence comparisons.
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Affiliation(s)
- Haihong Wang
- Department of Microbiology, University of Illinois, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
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Price AC, Zhang YM, Rock CO, White SW. Cofactor-induced conformational rearrangements establish a catalytically competent active site and a proton relay conduit in FabG. Structure 2004; 12:417-28. [PMID: 15016358 DOI: 10.1016/j.str.2004.02.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 11/11/2003] [Accepted: 11/14/2003] [Indexed: 11/27/2022]
Abstract
beta-Ketoacyl-acyl carrier protein reductase (FabG) is a key component in the type II fatty acid synthase system. The structures of Escherichia coli FabG and the FabG[Y151F] mutant in binary complexes with NADP(H) reveal that mechanistically important conformational changes accompany cofactor binding. The active site Ser-Tyr-Lys triad is repositioned into a catalytically competent constellation, and a hydrogen bonded network consisting of ribose hydroxyls, the Ser-Tyr-Lys triad, and four water molecules creates a proton wire to replenish the tyrosine proton donated during catalysis. Also, a disordered loop in FabG forms a substructure in the complex that shapes the entrance to the active site. A key observation is that the nicotinamide portion of the cofactor is disordered in the FabG[Y151F].NADP(H) complex, and Tyr151 appears to be necessary for high-affinity cofactor binding. Biochemical data confirm that FabG[Y151F] is defective in NADPH binding. Finally, structural changes consistent with the observed negative cooperativity of FabG are described.
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Affiliation(s)
- Allen C Price
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN 38105 USA
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Lu YJ, Zhang YM, Rock CO. Product diversity and regulation of type II fatty acid synthases. Biochem Cell Biol 2004; 82:145-55. [PMID: 15052334 DOI: 10.1139/o03-076] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Fatty acid biosynthesis is catalyzed in most bacteria by a group of highly conserved proteins known as the type II fatty acid synthase (FAS II) system. FAS II has been extensively studied in the Escherichia coli model system, and the recent explosion of bioinformatic information has accelerated the investigation of the pathway in other organisms, mostly important human pathogens. All FAS II systems possess a basic set of enzymes for the initiation and elongation of acyl chains. This review focuses on the variations on this basic theme that give rise to the diversity of products produced by the pathway. These include multiple mechanisms to generate unsaturated fatty acids and the accessory components required for branched-chain fatty acid synthesis in Gram-positive bacteria. Most of the known mechanisms that regulate product distribution of the pathway arise from the fundamental biochemical properties of the expressed enzymes. However, newly identified transcriptional factors in bacterial fatty acid biosynthetic pathways are a fertile field for new investigation into the genetic control of the FAS II system. Much more work is needed to define the role of these factors and the mechanisms that regulate their DNA binding capability, but there appear to be fundamental differences in how the expression of the pathway genes is controlled in Gram-negative and in Gram-positive bacteria.Key words: fatty acid synthase, bacteria.
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Affiliation(s)
- Ying-Jie Lu
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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