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Buyachuihan L, Stegemann F, Grininger M. How Acyl Carrier Proteins (ACPs) Direct Fatty Acid and Polyketide Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202312476. [PMID: 37856285 DOI: 10.1002/anie.202312476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Megasynthases, such as type I fatty acid and polyketide synthases (FASs and PKSs), are multienzyme complexes responsible for producing primary metabolites and complex natural products. Fatty acids (FAs) and polyketides (PKs) are built by assembling and modifying small acyl moieties in a stepwise manner. A central aspect of FA and PK biosynthesis involves the shuttling of substrates between the domains of the multienzyme complex. This essential process is mediated by small acyl carrier proteins (ACPs). The ACPs must navigate to the different catalytic domains within the multienzyme complex in a particular order to guarantee the fidelity of the biosynthesis pathway. However, the precise mechanisms underlying ACP-mediated substrate shuttling, particularly the factors contributing to the programming of the ACP movement, still need to be fully understood. This Review illustrates the current understanding of substrate shuttling, including concepts of conformational and specificity control, and proposes a confined ACP movement within type I megasynthases.
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Affiliation(s)
- Lynn Buyachuihan
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
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2
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Cho YI, Armstrong CL, Sulpizio A, Acheampong KK, Banks KN, Bardhan O, Churchill SJ, Connolly-Sporing AE, Crawford CE, Cruz Parrilla PL, Curtis SM, De La Ossa LM, Epstein SC, Farrehi CJ, Hamrick GS, Hillegas WJ, Kang A, Laxton OC, Ling J, Matsumura SM, Merino VM, Mukhtar SH, Shah NJ, Londergan CH, Daly CA, Kokona B, Charkoudian LK. Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins. Biochemistry 2022; 61:217-227. [PMID: 35073057 PMCID: PMC9357449 DOI: 10.1021/acs.biochem.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.
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Affiliation(s)
- Yae In Cho
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | - Oishi Bardhan
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | - Sarah M. Curtis
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | | | - Austin Kang
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Joie Ling
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | - Neel J. Shah
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Clyde A. Daly
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA 19041
- Spark Therapeutics, Philadelphia PA 19041
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3
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Patil R, Jadhav M, Salunke-Gawali S, Lande DN, Gejji SP, Chakravarty D. 1H and 13C NMR chemical shifts of 2- n-alkylamino-naphthalene-1,4-diones. Heliyon 2021; 7:e06044. [PMID: 33553738 PMCID: PMC7848645 DOI: 10.1016/j.heliyon.2021.e06044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/29/2020] [Accepted: 01/18/2021] [Indexed: 10/25/2022] Open
Abstract
1H as well as 13C chemical shifts of 32 compounds of C (3) substituted 2-(n-alkylamino)-3R-naphthalene-1,4-dione (where n-alkyl: methyl, to octyl, R = H, Cl, Br, and CH3) are investigated through 1H, 13C, DEPT, gDQCOSY, and gHSQCAD NMR experiments and M06-2X/6-311++G (d,p) density functional theory are discussed. Single crystal X-ray structure of Br-3, as well as 18 different derivatives of naphthalene-1,4-diones, are revealed for its inter and intra-molecular hydrogen bonding interactions.
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Affiliation(s)
- Rishikesh Patil
- Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
| | - Mahesh Jadhav
- Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
| | - Sunita Salunke-Gawali
- Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
| | - Dipali N Lande
- Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
| | - Shridhar P Gejji
- Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
| | - Debamitra Chakravarty
- Central Instrumentation Facility, Savitribai Phule Pune University, Pune, 411007, Maharashtra State, India
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4
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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5
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Paul S, Ishida H, Nguyen LT, Liu Z, Vogel HJ. Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics. Protein Sci 2017; 26:946-959. [PMID: 28187530 PMCID: PMC5405426 DOI: 10.1002/pro.3138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/08/2022]
Abstract
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Similar to the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme nonribosomal peptide synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding acyl carrier proteins (ACPs), for which the genes are located near to NRPS gene clusters. Here, we report that the solution NMR structure of apo-LipD is very similar to other four-helix bundle forming ACPs from fatty acid synthase (FAS), polyketide synthase, and NRPS systems. By recording NMR dynamics data, we found that the backbone motions in holo-LipD are more restricted than in apo-LipD due to the attachment of phosphopantetheine moiety. This enhanced stability of holo-LipD was also observed in differential scanning calorimetry experiments. Furthermore, we demonstrate that, unlike several other ACPs, the folding of LipD does not depend on the presence of divalent cations, although the presence of Mg2+ or Ca2+ can increase the protein stability. We propose that small structural rearrangements in the tertiary structure of holo-LipD which lead to the enhanced stability are important for the cognate enzyme recognition for the acylation reaction. Our results also highlight the different surface charges of LipD and FAS-ACP from A. friuliensis that would allow the acyl-CoA ligase to interact preferentially with the LipD instead of binding to the FAS-ACP.
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Affiliation(s)
- Subrata Paul
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hiroaki Ishida
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Leonard T. Nguyen
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Zhihong Liu
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hans J. Vogel
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
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Aznar-Moreno JA, Venegas-Calerón M, Martínez-Force E, Garcés R, Salas JJ. Acyl carrier proteins from sunflower (Helianthus annuus L.) seeds and their influence on FatA and FatB acyl-ACP thioesterase activities. PLANTA 2016; 244:479-90. [PMID: 27095109 DOI: 10.1007/s00425-016-2521-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/04/2016] [Indexed: 05/13/2023]
Abstract
The kinetics of acyl-ACP thioesterases from sunflower importantly changed when endogenous ACPs were used. Sunflower FatB was much more specific towards saturated acyl-ACPs when assayed with them. Acyl carrier proteins (ACPs) are small (~9 kDa), soluble, acidic proteins involved in fatty acid synthesis in plants and bacteria. ACPs bind to fatty acids through a thioester bond, generating the acyl-ACP lipoproteins that are substrates for fatty acid synthase (FAS) complexes, and that are required for fatty acid chain elongation, acting as important intermediates in de novo fatty acid synthesis in plants. Plants, usually express several ACP isoforms with distinct functionalities. We report here the cloning of three ACPs from developing sunflower seeds: HaACP1, HaACP2, and HaACP3. These proteins were plastidial ACPs expressed strongly in seeds, and as such they are probably involved in the synthesis of sunflower oil. The recombinant sunflower ACPs were expressed in bacteria but they were lethal to the prokaryote host. Thus, they were finally produced using the GST gene fusion system, which allowed the apo-enzyme to be produced and later activated to the holo form. Radiolabelled acyl-ACPs from the newly cloned holo-ACP forms were also synthesized and used to characterize the activity of recombinant sunflower FatA and FatB thioesterases, important enzymes in plant fatty acids synthesis. The activity of these enzymes changed significantly when the endogenous ACPs were used. Thus, FatA importantly increased its activity levels, whereas FatB displayed a different specificity profile, with much high activity levels towards saturated acyl-CoA derivatives. All these data pointed to an important influence of the ACP moieties on the activity of enzymes involved in lipid synthesis.
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Affiliation(s)
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1, 41013, Seville, Spain
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1, 41013, Seville, Spain
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1, 41013, Seville, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Carretera de Utrera Km 1, 41013, Seville, Spain.
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7
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Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase. Biochem J 2016; 473:1097-110. [PMID: 26920023 PMCID: PMC4847154 DOI: 10.1042/bcj20160041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/18/2016] [Indexed: 11/17/2022]
Abstract
When covalently linked to an acyl carrier protein (ACP) and loaded with acyl substrate-mimics, some 4′-phosphopantetheine prosthetic group arms swing freely, whereas others stick to the protein surface, suggesting a possible mode of interaction with enzyme domains during polyketide biosynthesis. Type I modular polyketide synthases (PKSs) produce polyketide natural products by passing a growing acyl substrate chain between a series of enzyme domains housed within a gigantic multifunctional polypeptide assembly. Throughout each round of chain extension and modification reactions, the substrate stays covalently linked to an acyl carrier protein (ACP) domain. In the present study we report on the solution structure and dynamics of an ACP domain excised from MLSA2, module 9 of the PKS system that constructs the macrolactone ring of the toxin mycolactone, cause of the tropical disease Buruli ulcer. After modification of apo ACP with 4′-phosphopantetheine (Ppant) to create the holo form, 15N nuclear spin relaxation and paramagnetic relaxation enhancement (PRE) experiments suggest that the prosthetic group swings freely. The minimal chemical shift perturbations displayed by Ppant-attached C3 and C4 acyl chains imply that these substrate-mimics remain exposed to solvent at the end of a flexible Ppant arm. By contrast, hexanoyl and octanoyl chains yield much larger chemical shift perturbations, indicating that they interact with the surface of the domain. The solution structure of octanoyl-ACP shows the Ppant arm bending to allow the acyl chain to nestle into a nonpolar pocket, whereas the prosthetic group itself remains largely solvent exposed. Although the highly reduced octanoyl group is not a natural substrate for the ACP from MLSA2, similar presentation modes would permit partner enzyme domains to recognize an acyl group while it is bound to the surface of its carrier protein, allowing simultaneous interactions with both the substrate and the ACP.
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8
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Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that have found widespread application as pharmaceuticals, agrochemicals, and veterinary medicines. In bacteria complex polyketides are biosynthesized by giant multifunctional megaenzymes, termed modular polyketide synthases (PKSs), which construct their products in a highly coordinated assembly line-like fashion from a pool of simple precursor substrates. Not only is the multifaceted enzymology of PKSs a fascinating target for study, but it also presents considerable opportunities for the reengineering of these systems affording access to functionally optimized unnatural natural products. Here we provide an introductory primer to modular polyketide synthase structure and function, and highlight recent advances in the characterization and exploitation of these systems.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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9
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Park YG, Jung MC, Song H, Jeong KW, Bang E, Hwang GS, Kim Y. Novel Structural Components Contribute to the High Thermal Stability of Acyl Carrier Protein from Enterococcus faecalis. J Biol Chem 2015; 291:1692-1702. [PMID: 26631734 DOI: 10.1074/jbc.m115.674408] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/06/2022] Open
Abstract
Enterococcus faecalis is a Gram-positive, commensal bacterium that lives in the gastrointestinal tracts of humans and other mammals. It causes severe infections because of high antibiotic resistance. E. faecalis can endure extremes of temperature and pH. Acyl carrier protein (ACP) is a key element in the biosynthesis of fatty acids responsible for acyl group shuttling and delivery. In this study, to understand the origin of high thermal stabilities of E. faecalis ACP (Ef-ACP), its solution structure was investigated for the first time. CD experiments showed that the melting temperature of Ef-ACP is 78.8 °C, which is much higher than that of Escherichia coli ACP (67.2 °C). The overall structure of Ef-ACP shows the common ACP folding pattern consisting of four α-helices (helix I (residues 3-17), helix II (residues 39-53), helix III (residues 60-64), and helix IV (residues 68-78)) connected by three loops. Unique Ef-ACP structural features include a hydrophobic interaction between Phe(45) in helix II and Phe(18) in the α1α2 loop and a hydrogen bonding between Ser(15) in helix I and Ile(20) in the α1α2 loop, resulting in its high thermal stability. Phe(45)-mediated hydrophobic packing may block acyl chain binding subpocket II entry. Furthermore, Ser(58) in the α2α3 loop in Ef-ACP, which usually constitutes a proline in other ACPs, exhibited slow conformational exchanges, resulting in the movement of the helix III outside the structure to accommodate a longer acyl chain in the acyl binding cavity. These results might provide insights into the development of antibiotics against pathogenic drug-resistant E. faecalis strains.
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Affiliation(s)
- Young-Guen Park
- From the Department of Bioscience and Biotechnology and the Bio/Molecular Informatics Center Konkuk University, Seoul 143-701, Korea and
| | - Min-Cheol Jung
- From the Department of Bioscience and Biotechnology and the Bio/Molecular Informatics Center Konkuk University, Seoul 143-701, Korea and
| | - Heesang Song
- From the Department of Bioscience and Biotechnology and the Bio/Molecular Informatics Center Konkuk University, Seoul 143-701, Korea and
| | - Ki-Woong Jeong
- From the Department of Bioscience and Biotechnology and the Bio/Molecular Informatics Center Konkuk University, Seoul 143-701, Korea and
| | - Eunjung Bang
- the Western Seoul Center, Korea Basic Science Institute, Seoul 120-140, Korea
| | - Geum-Sook Hwang
- the Western Seoul Center, Korea Basic Science Institute, Seoul 120-140, Korea
| | - Yangmee Kim
- From the Department of Bioscience and Biotechnology and the Bio/Molecular Informatics Center Konkuk University, Seoul 143-701, Korea and.
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10
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Goodrich AC, Harden BJ, Frueh DP. Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts. J Am Chem Soc 2015; 137:12100-9. [PMID: 26334259 DOI: 10.1021/jacs.5b07772] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are microbial enzymes that produce a wealth of important natural products by condensing substrates in an assembly line manner. The proper sequence of substrates is obtained by tethering them to phosphopantetheinyl arms of holo carrier proteins (CPs) via a thioester bond. CPs in holo and substrate-loaded forms visit NRPS catalytic domains in a series of transient interactions. A lack of structural information on substrate-loaded carrier proteins has hindered our understanding of NRPS synthesis. Here, we present the first structure of an NRPS aryl carrier protein loaded with its substrate via a native thioester bond, together with the structure of its holo form. We also present the first quantification of NRPS CP backbone dynamics. Our results indicate that prosthetic moieties in both holo and loaded forms are in contact with the protein core, but they also sample states in which they are disordered and extend in solution. We observe that substrate loading induces a large conformational change in the phosphopantetheinyl arm, thereby modulating surfaces accessible for binding to other domains. Our results are discussed in the context of NRPS domain interactions.
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Affiliation(s)
- Andrew C Goodrich
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Bradley J Harden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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Kumar A, Arya R, Makwana PK, Dangi RS, Yadav U, Surolia A, Kundu S, Sundd M. The Structure of the Holo-Acyl Carrier Protein of Leishmania major Displays a Remarkably Different Phosphopantetheinyl Transferase Binding Interface. Biochemistry 2015; 54:5632-45. [DOI: 10.1021/acs.biochem.5b00394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ambrish Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Richa Arya
- Department
of Biochemistry, University of Delhi South Campus, Benito Juarez
Road, New Delhi 110 021, India
| | - Pinakin K. Makwana
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Rohit Singh Dangi
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Usha Yadav
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Avadhesha Surolia
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Suman Kundu
- Department
of Biochemistry, University of Delhi South Campus, Benito Juarez
Road, New Delhi 110 021, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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12
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Johnson MR, Londergan CH, Charkoudian LK. Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy. J Am Chem Soc 2014; 136:11240-3. [PMID: 25080832 PMCID: PMC4140477 DOI: 10.1021/ja505442h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 12/23/2022]
Abstract
Acyl carrier proteins (ACPs) are universal and highly conserved domains central to both fatty acid and polyketide biosynthesis. These proteins tether reactive acyl intermediates with a swinging 4'-phosphopantetheine (Ppant) arm and interact with a suite of catalytic partners during chain transport and elongation while stabilizing the growing chain throughout the biosynthetic pathway. The flexible nature of the Ppant arm and the transient nature of ACP-enzyme interactions impose a major obstacle to obtaining structural information relevant to understanding polyketide and fatty acid biosynthesis. To overcome this challenge, we installed a thiocyanate vibrational spectroscopic probe on the terminal thiol of the ACP Ppant arm. This site-specific probe successfully reported on the local environment of the Ppant arm of two ACPs previously characterized by solution NMR, and was used to determine the solution exposure of the Ppant arm of an ACP from 6-deoxyerythronolide B synthase (DEBS). Given the sensitivity of the probe's CN stretching band to conformational distributions resolved on the picosecond time scale, this work lays a foundation for observing the dynamic action-related structural changes of ACPs using vibrational spectroscopy.
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Affiliation(s)
- Matthew
N. R. Johnson
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
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13
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Javidpour P, Bruegger J, Srithahan S, Korman TP, Crump MP, Crosby J, Burkart MD, Tsai SC. The determinants of activity and specificity in actinorhodin type II polyketide ketoreductase. ACTA ACUST UNITED AC 2013; 20:1225-34. [PMID: 24035284 DOI: 10.1016/j.chembiol.2013.07.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 11/17/2022]
Abstract
In the actinorhodin type II polyketide synthase, the first polyketide modification is a regiospecific C9-carbonyl reduction, catalyzed by the ketoreductase (actKR). Our previous studies identified the actKR 94-PGG-96 motif as a determinant of stereospecificity. The molecular basis for reduction regiospecificity is, however, not well understood. In this study, we examined the activities of 20 actKR mutants through a combination of kinetic studies, PKS reconstitution, and structural analyses. Residues have been identified that are necessary for substrate interaction, and these observations have suggested a structural model for this reaction. Polyketides dock at the KR surface and are steered into the enzyme pocket where C7-C12 cyclization is mediated by the KR before C9-ketoreduction can occur. These molecular features can potentially serve as engineering targets for the biosynthesis of novel, reduced polyketides.
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Affiliation(s)
- Pouya Javidpour
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
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14
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Metsä-Ketelä M, Oja T, Taguchi T, Okamoto S, Ichinose K. Biosynthesis of pyranonaphthoquinone polyketides reveals diverse strategies for enzymatic carbon–carbon bond formation. Curr Opin Chem Biol 2013; 17:562-70. [DOI: 10.1016/j.cbpa.2013.06.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
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15
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Lim J, Sun H, Fan JS, Hameed IF, Lescar J, Liang ZX, Yang D. Rigidifying acyl carrier protein domain in iterative type I PKS CalE8 does not affect its function. Biophys J 2013; 103:1037-44. [PMID: 23009853 DOI: 10.1016/j.bpj.2012.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 10/27/2022] Open
Abstract
Acyl carrier protein (ACP) domains shuttle acyl intermediates among the catalytic domains of multidomain type I fatty acid synthase and polyketide synthase (PKS) systems. It is believed that the unique function of ACPs is associated with their dynamic property, but it remains to be fully elucidated what type of protein dynamics is critical for the shuttling domain. Using NMR techniques, we found that the ACP domain of iterative type I PKS CalE8 from Micromonospora echinospora is highly dynamic on the millisecond-second timescale. Introduction of an interhelical disulfide linkage in the ACP domain suppresses the dynamics on the millisecond-second timescale and reduces the mobility on the picosecond-nanosecond timescale. We demonstrate that the full-length PKS is fully functional upon rigidification of the ACP domain, suggesting that although the flexibility of the disordered terminal linkers may be important for the function of the ACP domain, the internal dynamics of the helical regions is not critical for that function.
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Affiliation(s)
- Jackwee Lim
- Department of Biological Sciences, National University of Singapore, Singapore
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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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Ramelot TA, Rossi P, Forouhar F, Lee HW, Yang Y, Ni S, Unser S, Lew S, Seetharaman J, Xiao R, Acton TB, Everett JK, Prestegard JH, Hunt JF, Montelione GT, Kennedy MA. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations. Biochemistry 2012; 51:7239-49. [PMID: 22876860 DOI: 10.1021/bi300546b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States.
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18
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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19
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Busche A, Gottstein D, Hein C, Ripin N, Pader I, Tufar P, Eisman EB, Gu L, Walsh CT, Sherman DH, Löhr F, Güntert P, Dötsch V. Characterization of molecular interactions between ACP and halogenase domains in the Curacin A polyketide synthase. ACS Chem Biol 2012; 7:378-86. [PMID: 22103656 DOI: 10.1021/cb200352q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are large multidomain proteins present in microorganisms that produce bioactive compounds. Curacin A is such a bioactive compound with potent anti-proliferative activity. During its biosynthesis the growing substrate is bound covalently to an acyl carrier protein (ACP) that is able to access catalytic sites of neighboring domains for chain elongation and modification. While ACP domains usually occur as monomers, the curacin A cluster codes for a triplet ACP (ACP(I)-ACP(II)-ACP(III)) within the CurA PKS module. We have determined the structure of the isolated holo-ACP(I) and show that the ACPs are independent of each other within this tridomain system. In addition, we have determined the structure of the 3-hydroxyl-3-methylglutaryl-loaded holo-ACP(I), which is the substrate for the unique halogenase (Hal) domain embedded within the CurA module. We have identified the interaction surface of both proteins using mutagenesis and MALDI-based identification of product formation. Amino acids affecting product formation are located on helices II and III of ACP(I) and form a contiguous surface. Since the CurA Hal accepts substrate only when presented by one of the ACPs within the ACP(I)-ACP(II)-ACP(III) tridomain, our data provide insight into the specificity of the chlorination reaction.
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Affiliation(s)
- Alena Busche
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Daniel Gottstein
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Nina Ripin
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Irina Pader
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Peter Tufar
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Eli B. Eisman
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Liangcai Gu
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | | | - David H. Sherman
- Life Sciences Institute,
Departments
of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Frank Löhr
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
- Frankfurt
Institute for Advanced
Studies, Goethe University Frankfurt, Ruth-Moufang-Str.
1, 60438 Frankfurt am Main, Germany
- Center for Priority Areas, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University Frankfurt and Center for Biomolecular
Magnetic Resonance, Max-von-Laue Str. 9, 60438 Frankfurt am Main,
Germany
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20
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Dharmaraja AT, Dash TK, Konkimalla VB, Chakrapani H. Synthesis, thiol-mediated reactive oxygen species generation profiles and anti-proliferative activities of 2,3-epoxy-1,4-naphthoquinones. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00234a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Liu Y, Zheng T, Bruner SD. Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases. CHEMISTRY & BIOLOGY 2011; 18:1482-8. [PMID: 22118682 PMCID: PMC3238681 DOI: 10.1016/j.chembiol.2011.09.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/14/2011] [Accepted: 09/26/2011] [Indexed: 01/07/2023]
Abstract
Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides, and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here, we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of Escherichia coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain.
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Affiliation(s)
- Ye Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Tengfei Zheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA 32611,Correspondence: Steven Bruner, , (352) 392-0525
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22
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Ames BD, Lee MY, Moody C, Zhang W, Tang Y, Tsai SC. Structural and biochemical characterization of ZhuI aromatase/cyclase from the R1128 polyketide pathway. Biochemistry 2011; 50:8392-406. [PMID: 21870821 DOI: 10.1021/bi200593m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aromatic polyketides comprise an important class of natural products that possess a wide range of biological activities. The cyclization of the polyketide chain is a critical control point in the biosynthesis of aromatic polyketides. The aromatase/cyclases (ARO/CYCs) are an important component of the type II polyketide synthase (PKS) and help fold the polyketide for regiospecific cyclizations of the first ring and/or aromatization, promoting two commonly observed first-ring cyclization patterns for the bacterial type II PKSs: C7-C12 and C9-C14. We had previously reported the crystal structure and enzymological analyses of the TcmN ARO/CYC, which promotes C9-C14 first-ring cyclization. However, how C7-C12 first-ring cyclization is controlled remains unresolved. In this work, we present the 2.4 Å crystal structure of ZhuI, a C7-C12-specific first-ring ARO/CYC from the type II PKS pathway responsible for the production of the R1128 polyketides. Though ZhuI possesses a helix-grip fold shared by TcmN ARO/CYC, there are substantial differences in overall structure and pocket residue composition that may be important for directing C7-C12 (rather than C9-C14) cyclization. Docking studies and site-directed mutagenesis coupled to an in vitro activity assay demonstrate that ZhuI pocket residues R66, H109, and D146 are important for enzyme function. The ZhuI crystal structure helps visualize the structure and putative dehydratase function of the didomain ARO/CYCs from KR-containing type II PKSs. The sequence-structure-function analysis described for ZhuI elucidates the molecular mechanisms that control C7-C12 first-ring polyketide cyclization and builds a foundation for future endeavors into directing cyclization patterns for engineered biosynthesis of aromatic polyketides.
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Affiliation(s)
- Brian D Ames
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
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23
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Solution structures of the acyl carrier protein domain from the highly reducing type I iterative polyketide synthase CalE8. PLoS One 2011; 6:e20549. [PMID: 21674045 PMCID: PMC3107222 DOI: 10.1371/journal.pone.0020549] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 05/03/2011] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of the enediyne natural product calicheamicins γ1I in Micromonospora echinospora ssp. calichensis is initiated by the iterative polyketide synthase (PKS) CalE8. Recent studies showed that CalE8 produces highly conjugated polyenes as potential biosynthetic intermediates and thus belongs to a family of highly-reducing (HR) type I iterative PKSs. We have determined the NMR structure of the ACP domain (meACP) of CalE8, which represents the first structure of a HR type I iterative PKS ACP domain. Featured by a distinct hydrophobic patch and a glutamate-residue rich acidic patch, meACP adopts a twisted three-helix bundle structure rather than the canonical four-helix bundle structure. The so-called ‘recognition helix’ (α2) of meACP is less negatively charged than the typical type II ACPs. Although loop-2 exhibits greater conformational mobility than other regions of the protein with a missing short helix that can be observed in most ACPs, two bulky non-polar residues (Met992, Phe996) from loop-2 packed against the hydrophobic protein core seem to restrict large movement of the loop and impede the opening of the hydrophobic pocket for sequestering the acyl chains. NMR studies of the hydroxybutyryl- and octanoyl-meACP confirm that meACP is unable to sequester the hydrophobic chains in a well-defined central cavity. Instead, meACP seems to interact with the octanoyl tail through a distinct hydrophobic patch without involving large conformational change of loop-2. NMR titration study of the interaction between meACP and the cognate thioesterase partner CalE7 further suggests that their interaction is likely through the binding of CalE7 to the meACP-tethered polyene moiety rather than direct specific protein-protein interaction.
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24
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Haushalter RW, Filipp FV, Ko KS, Yu R, Opella SJ, Burkart MD. Binding and "pKa" modulation of a polycyclic substrate analogue in a type II polyketide acyl carrier protein. ACS Chem Biol 2011; 6:413-8. [PMID: 21268653 DOI: 10.1021/cb200004k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Type II polyketide synthases are biosynthetic enzymatic pathways responsible for the production of complex aromatic natural products with important biological activities. In these systems, biosynthetic intermediates are covalently bound to a small acyl carrier protein that associates with the synthase enzymes and delivers the bound intermediate to each active site. In the closely related fatty acid synthases of bacteria and plants, the acyl carrier protein acts to sequester and protect attached intermediates within its helices. Here we investigate the type II polyketide synthase acyl carrier protein from the actinorhodin biosynthetic pathway and demonstrate its ability to internalize the tricyclic, polar molecule emodic acid. Elucidating the interaction of acyl carrier proteins with bound analogues resembling late-stage intermediates in the actinorhodin pathway could prove valuable in efforts to engineer these systems toward rational design and biosynthesis of novel compounds.
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Affiliation(s)
- Robert W. Haushalter
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Fabian V. Filipp
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Kwang-seuk Ko
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Ricky Yu
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States
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25
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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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26
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Worthington AS, Porter DF, Burkart MD. Mechanism-based crosslinking as a gauge for functional interaction of modular synthases. Org Biomol Chem 2010; 8:1769-72. [PMID: 20449476 DOI: 10.1039/b925966j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein-protein interactions between domains within fatty acid and polyketide synthases are critical to catalysis, but their contributions remain incompletely characterized. A practical, quantitative system for establishing functional interactions between modifying enzymes and the acyl carrier protein that tethers the nascent polymer would offer a valuable tool for understanding and engineering these enzyme systems. Mechanism-based crosslinking of modular domains offers a potential diagnostic to highlight selective interactions between modular pairs. Here kinetic activity analysis and isothermal titration calorimetry are shown to correlate the efficiency of a ketosynthase-carrier protein crosslinking method to the binding affinity and transacylase activity that occurs in ketosynthase chain elongation.
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Affiliation(s)
- Andrew S Worthington
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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27
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Tran L, Broadhurst RW, Tosin M, Cavalli A, Weissman KJ. Insights into Protein-Protein and Enzyme-Substrate Interactions in Modular Polyketide Synthases. ACTA ACUST UNITED AC 2010; 17:705-16. [DOI: 10.1016/j.chembiol.2010.05.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/26/2010] [Accepted: 05/03/2010] [Indexed: 11/29/2022]
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28
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Wattana-amorn P, Williams C, Płoskoń E, Cox RJ, Simpson TJ, Crosby J, Crump MP. Solution Structure of an Acyl Carrier Protein Domain from a Fungal Type I Polyketide Synthase,. Biochemistry 2010; 49:2186-93. [DOI: 10.1021/bi902176v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pakorn Wattana-amorn
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Christopher Williams
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Eliza Płoskoń
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Russell J. Cox
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Thomas J. Simpson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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29
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Shields JA, Rahman AS, Arthur CJ, Crosby J, Hothersall J, Simpson TJ, Thomas CM. Phosphopantetheinylation and Specificity of Acyl Carrier Proteins in the Mupirocin Biosynthetic Cluster. Chembiochem 2009; 11:248-55. [DOI: 10.1002/cbic.200900565] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Wu BN, Zhang YM, Rock CO, Zheng JJ. Structural modification of acyl carrier protein by butyryl group. Protein Sci 2009; 18:240-6. [PMID: 19177367 DOI: 10.1002/pro.11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fatty acid synthesis in bacteria is catalyzed by a set of individual enzymes known as the type II fatty acid synthase. Acyl carrier protein (ACP) shuttles the acyl intermediates between individual pathway enzymes. In this study, we determined the solution structures of three different forms of ACP, apo-ACP, ACP, and butyryl-ACP under identical experimental conditions. The structural studies revealed that attachment of butyryl acyl intermediate to ACP alters the conformation of ACP. This finding supports the more general notion that the attachment of different acyl intermediates alters the ACP structure to facilitate their recognition and turnover by the appropriate target enzymes.
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Affiliation(s)
- Bai-Nan Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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31
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Upadhyay SK, Misra A, Srivastava R, Surolia N, Surolia A, Sundd M. Structural insights into the acyl intermediates of the Plasmodium falciparum fatty acid synthesis pathway: the mechanism of expansion of the acyl carrier protein core. J Biol Chem 2009; 284:22390-22400. [PMID: 19520851 DOI: 10.1074/jbc.m109.014829] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acyl carrier protein (ACP) plays a central role in fatty acid biosynthesis. However, the molecular machinery that mediates its function is not yet fully understood. Therefore, structural studies were carried out on the acyl-ACP intermediates of Plasmodium falciparum using NMR as a spectroscopic probe. Chemical shift perturbation studies put forth a new picture of the interaction of ACP molecule with the acyl chain, namely, the hydrophobic core can protect up to 12 carbon units, and additional carbons protrude out from the top of the hydrophobic cavity. The latter hypothesis stems from chemical shift changes observed in Calpha and Cbeta of Ser-37 in tetradecanoyl-ACP. 13C,15N-Double-filtered nuclear Overhauser effect (NOE) spectroscopy experiments further substantiate the concept; in octanoyl (C8)- and dodecanoyl (C12)-ACP, a long range NOE is observed within the phosphopantetheine arm, suggesting an arch-like conformation. This NOE is nearly invisible in tetradecanoyl (C14)-ACP, indicating a change in conformation of the prosthetic group. Furthermore, the present study provides insights into the molecular mechanism of ACP expansion, as revealed from a unique side chain-to-backbone hydrogen bond between two fairly conserved residues, Ile-55 HN and Glu-48 O. The backbone amide of Ile-55 HN reports a pKa value for the carboxylate, approximately 1.9 pH units higher than model compound value, suggesting strong electrostatic repulsion between helix II and helix III. Charge-charge repulsion between the helices in combination with thrust from inside due to acyl chain would energetically favor the separation of the two helices. Helix III has fewer structural restraints and, hence, undergoes major conformational change without altering the overall-fold of P. falciparum ACP.
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Affiliation(s)
| | - Ashish Misra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012
| | - Richa Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012
| | - Namita Surolia
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore 560064, India
| | - Avadhesha Surolia
- National Institute of Immunology, New Delhi 110067; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012
| | - Monica Sundd
- National Institute of Immunology, New Delhi 110067
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32
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Evans SE, Williams C, Arthur CJ, Płoskoń E, Wattana-amorn P, Cox RJ, Crosby J, Willis CL, Simpson TJ, Crump MP. Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2). J Mol Biol 2009; 389:511-28. [DOI: 10.1016/j.jmb.2009.03.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 03/25/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
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Abstract
Natural products, produced chiefly by microorganisms and plants, can be large and structurally complex molecules. These molecules are manufactured by cellular assembly lines, in which enzymes construct the molecules in a stepwise fashion. The means by which enzymes interact and work together in a modular fashion to create diverse structural features has been an active area of research; the work has provided insight into the fine details of biosynthesis. A number of polycyclic aromatic natural products--including several noteworthy anticancer, antibacterial, antifungal, antiviral, antiparasitic, and other medicinally significant substances--are synthesized by polyketide synthases (PKSs) in soil-borne bacteria called actinomycetes. Concerted biosynthetic, enzymological, and structural biological investigations into these modular enzyme systems have yielded interesting mechanistic insights. A core module called the minimal PKS is responsible for synthesizing a highly reactive, protein-bound poly-beta-ketothioester chain. In the absence of other enzymes, the minimal PKS also catalyzes chain initiation and release, yielding an assortment of polycyclic aromatic compounds. In the presence of an initiation PKS module, polyketide backbones bearing additional alkyl, alkenyl, or aryl primer units are synthesized, whereas a range of auxiliary PKS enzymes and tailoring enzymes convert the product of the minimal PKS into the final natural product. In this Account, we summarize the knowledge that has been gained regarding this family of PKSs through recent investigations into the biosynthetic pathways of two natural products, actinorhodin and R1128 (A-D). We also discuss the practical relevance of these fundamental insights for the engineered biosynthesis of new polycyclic aromatic compounds. With a deeper understanding of the biosynthetic process in hand, we can assert control at various stages of molecular construction and thus introduce unnatural functional groups in the process. The metabolic engineer affords a number of new avenues for creating novel molecular structures that will likely have properties akin to their fully natural cousins.
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Affiliation(s)
| | - Chaitan Khosla
- Department of Chemistry
- Department of Chemical Engineering
- Department of Biochemistry, Stanford University, Stanford, California 94305-5025
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Khosla C, Kapur S, Cane DE. Revisiting the modularity of modular polyketide synthases. Curr Opin Chem Biol 2009; 13:135-43. [PMID: 19217343 DOI: 10.1016/j.cbpa.2008.12.018] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 12/25/2008] [Indexed: 11/28/2022]
Abstract
Modularity is a highly sought after feature in engineering design. A modular catalyst is a multi-component system whose parts can be predictably interchanged for functional flexibility and variety. Nearly two decades after the discovery of the first modular polyketide synthase (PKS), we critically assess PKS modularity in the face of a growing body of atomic structural and in vitro biochemical investigations. Both the architectural modularity and the functional modularity of this family of enzymatic assembly lines are reviewed, and the fundamental challenges that lie ahead for the rational exploitation of their full biosynthetic potential are discussed.
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Affiliation(s)
- Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
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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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36
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Castaldo G, Zucko J, Heidelberger S, Vujaklija D, Hranueli D, Cullum J, Wattana-Amorn P, Crump MP, Crosby J, Long PF. Proposed Arrangement of Proteins Forming a Bacterial Type II Polyketide Synthase. ACTA ACUST UNITED AC 2008; 15:1156-65. [DOI: 10.1016/j.chembiol.2008.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 08/09/2008] [Accepted: 09/04/2008] [Indexed: 11/16/2022]
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37
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Evans SE, Williams C, Arthur CJ, Burston SG, Simpson TJ, Crosby J, Crump MP. An ACP Structural Switch: Conformational Differences between the Apo and Holo Forms of the Actinorhodin Polyketide Synthase Acyl Carrier Protein. Chembiochem 2008; 9:2424-32. [DOI: 10.1002/cbic.200800180] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Magarvey NA, Fortin PD, Thomas PM, Kelleher NL, Walsh CT. Gatekeeping versus promiscuity in the early stages of the andrimid biosynthetic assembly line. ACS Chem Biol 2008; 3:542-54. [PMID: 18652473 DOI: 10.1021/cb800085g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The antibiotic andrimid, a nanomolar inhibitor of bacterial acetyl coenzyme A carboxylase, is generated on an unusual polyketide/nonribosomal peptide enzyme assembly line in that all thiolation (T) domains/small-molecule building stations are on separate proteins. In addition, a transglutaminase homologue is used to condense andrimid building blocks together on the andrimid assembly line. The first two modules of the andrimid assembly line yields an octatrienoyl-beta-Phe-thioester tethered to the AdmI T domain, with amide bond formation carried out by a free-standing transglutaminase homologue AdmF. Analysis of the aminomutase AdmH reveals its specific conversion from l-Phe to (S)-beta-Phe, which in turn is activated by AdmJ and ATP to form (S)-beta-Phe-aminoacyl-AMP. AdmJ then transfers the (S)-beta-Phe moiety to one of the free-standing T domains, AdmI, but not AdmA, which instead gets loaded with an octatrienoyl group by other enzymes. AdmF, the amide synthase, will accept a variety of acyl groups in place of the octatrienoyl donor if presented on either AdmA or AdmI. AdmF will also use either stereoisomer of phenylalanine or beta-Phe when presented on AdmA and AdmI, but not when placed on noncognate T domains. Further, we show the polyketide synthase proteins responsible for the polyunsaturated acyl cap can be bypassed in vitro with N-acetylcysteamine as a low-molecular-weight acyl donor to AdmF and also in vivo in an Escherichia coli strain bearing the andrimid biosynthetic gene cluster with a knockout in admA.
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Affiliation(s)
- Nathan A. Magarvey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Pascal D. Fortin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Paul M. Thomas
- Department of Chemistry, University of Illinois, Urbana−Champaign, Illinois 61801
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois, Urbana−Champaign, Illinois 61801
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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Huang SW, Shih CH, Lin CP, Hwang JK. Prediction of NMR order parameters in proteins using weighted protein contact-number model. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0465-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Tran L, Tosin M, Spencer JB, Leadlay PF, Weissman KJ. Covalent linkage mediates communication between ACP and TE domains in modular polyketide synthases. Chembiochem 2008; 9:905-15. [PMID: 18348128 DOI: 10.1002/cbic.200700738] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Polyketide natural products such as erythromycin A and epothilone are assembled on multienzyme polyketide synthases (PKSs), which consist of modular sets of protein domains. Within these type I systems, the fidelity of biosynthesis depends on the programmed interaction among the multiple domains within each module, centered around the acyl carrier protein (ACP). A detailed understanding of interdomain communication will therefore be vital for attempts to reprogram these pathways by genetic engineering. We report here that the interaction between a representative ACP domain and its downstream thioesterase (TE) is mediated largely by covalent tethering through a short "linker" region, with only a minor energetic contribution from protein-protein molecular recognition. This finding helps explain in part the empirical observation that TE domains can function out of their normal context in engineered assembly lines, and supports the view that overall PKS architecture may dictate at least a subset of interdomain interactions.
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Affiliation(s)
- Lucky Tran
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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41
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Trott O, Siggers K, Rost B, Palmer AG. Protein conformational flexibility prediction using machine learning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:37-47. [PMID: 18313957 PMCID: PMC2413295 DOI: 10.1016/j.jmr.2008.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 12/15/2007] [Accepted: 01/26/2008] [Indexed: 05/26/2023]
Abstract
Using a data set of 16 proteins, a neural network has been trained to predict backbone 15N generalized order parameters from the three-dimensional structures of proteins. The final network parameterization contains six input features. The average prediction accuracy, as measured by the Pearson's correlation coefficient between experimental and predicted values of the square of the generalized order parameter is >0.70. Predicted order parameters for non-terminal amino acid residues depends most strongly on the local packing density and the probability that the residue is located in regular secondary structure.
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Affiliation(s)
| | | | | | - Arthur G. Palmer
- * Corresponding author. Fax: (212) 305-6949. E-mail address: (A. G. Palmer)
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42
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Weissman KJ, Müller R. Protein–Protein Interactions in Multienzyme Megasynthetases. Chembiochem 2008; 9:826-48. [DOI: 10.1002/cbic.200700751] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Ploskoń E, Arthur CJ, Evans SE, Williams C, Crosby J, Simpson TJ, Crump MP. A Mammalian Type I Fatty Acid Synthase Acyl Carrier Protein Domain Does Not Sequester Acyl Chains. J Biol Chem 2008; 283:518-528. [DOI: 10.1074/jbc.m703454200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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44
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Alekseyev VY, Liu CW, Cane DE, Puglisi JD, Khosla C. Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Sci 2007; 16:2093-107. [PMID: 17893358 PMCID: PMC2204127 DOI: 10.1110/ps.073011407] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide-producing assemblies. However, impaired domain-domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these domain-domain interactions, we have used nuclear magnetic resonance (NMR) spectroscopy to determine the first solution structure of an acyl carrier protein (ACP) domain from a modular PKS, 6-deoxyerythronolide B synthase (DEBS). The tertiary fold of this 10-kD domain is a three-helical bundle; an additional short helix in the second loop also contributes to the core helical packing. Superposition of residues 14-94 of the ensemble on the mean structure yields an average atomic RMSD of 0.64 +/- 0.09 Angstrom for the backbone atoms (1.21 +/- 0.13 Angstrom for all non-hydrogen atoms). The three major helices superimpose with a backbone RMSD of 0.48 +/- 0.10 Angstrom (0.99 +/- 0.11 Angstrom for non-hydrogen atoms). Based on this solution structure, homology models were constructed for five other DEBS ACP domains. Comparison of their steric and electrostatic surfaces at the putative interaction interface (centered on helix II) suggests a model for protein-protein recognition of ACP domains, consistent with the previously observed specificity. Site-directed mutagenesis experiments indicate that two of the identified residues influence the specificity of ACP recognition.
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Affiliation(s)
- Viktor Y Alekseyev
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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45
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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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46
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Tang Y, Chen AY, Kim CY, Cane DE, Khosla C. Structural and mechanistic analysis of protein interactions in module 3 of the 6-deoxyerythronolide B synthase. CHEMISTRY & BIOLOGY 2007; 14:931-43. [PMID: 17719492 PMCID: PMC1986752 DOI: 10.1016/j.chembiol.2007.07.012] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 07/10/2007] [Accepted: 07/13/2007] [Indexed: 11/20/2022]
Abstract
We report the 2.6 A X-ray crystal structure of a 190 kDa homodimeric fragment from module 3 of the 6-deoxyerthronolide B synthase covalently bound to the inhibitor cerulenin. The structure shows two well-organized interdomain linker regions in addition to the full-length ketosynthase (KS) and acyltransferase (AT) domains. Analysis of the substrate-binding site of the KS domain suggests that a loop region at the homodimer interface influences KS substrate specificity. We also describe a model for the interaction of the catalytic domains with the acyl carrier protein (ACP) domain. The ACP is proposed to dock within a deep cleft between the KS and AT domains, with interactions that span both the KS homodimer and AT domain. In conjunction with other recent data, our results provide atomic resolution pictures of several catalytically relevant protein interactions in this remarkable family of modular megasynthases.
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Affiliation(s)
- Yinyan Tang
- Departments of Chemistry and Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Alice Y. Chen
- Departments of Chemistry and Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Chu-Young Kim
- Departments of Chemistry and Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - David E. Cane
- Department of Chemistry, Brown University, Providence, Rhode Island 02912-9108, USA
| | - Chaitan Khosla
- Departments of Chemistry and Chemical Engineering, Stanford University, Stanford, California 94305, USA
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47
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Zhou Z, Cironi P, Lin AJ, Xu Y, Hrvatin S, Golan DE, Silver PA, Walsh CT, Yin J. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. ACS Chem Biol 2007; 2:337-46. [PMID: 17465518 DOI: 10.1021/cb700054k] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short peptide tags S6 and A1, each 12 residues in length, were identified from a phage-displayed peptide library as efficient substrates for site-specific protein labeling catalyzed by Sfp and AcpS phosphopantetheinyl transferases (PPTases), respectively. S6 and A1 tags were selected for useful levels of orthogonality in reactivities with the PPTases: the catalytic efficiency, kcat/Km of Sfp-catalyzed S6 serine phosphopantetheinylation was 442-fold greater than that for AcpS. Conversely, the kcat/Km of AcpS-catalyzed A1 labeling was 30-fold higher than that for Sfp-catalyzed A1 labeling. S6 and A1 peptide tags can be fused to N- or C-termini of proteins for orthogonal labeling of target proteins in cell lysates or on live cell surfaces. The development of the orthogonal S6 and A1 tags represents a significant enhancement of PPTase-catalyzed protein labeling, allowing tandem or iterative covalent attachment of small molecules of diverse structures to the target proteins with high efficiency and specificity.
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Affiliation(s)
- Zhe Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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48
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Mercer AC, Burkart MD. The ubiquitous carrier protein--a window to metabolite biosynthesis. Nat Prod Rep 2007; 24:750-73. [PMID: 17653358 DOI: 10.1039/b603921a] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nature has developed a remarkable strategy to isolate metabolites from the milieu of the cell for chemical modification through the use of carrier proteins. Common to both primary and secondary metabolic pathways, acyl-carrier proteins constitute a conserved protein architecture which mediate the biosynthesis of a variety of metabolic products. Analogies have been made between the carrier protein and solid phase resin for chemical synthesis, as both entities provide a mechanism to separate compounds of interest from complex mixtures for selective chemical modification. However, there is significantly more to the carrier protein than an attachment point. In this review, we aim to systematically characterize the role of carrier proteins in various metabolic pathways and outline their utility in biosynthesis and biotechnology; 185 references are cited.
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Affiliation(s)
- Andrew C Mercer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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49
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Fedoryshyn M, Nur-e-Alam M, Zhu L, Luzhetskyy A, Rohr J, Bechthold A. Surprising production of a new urdamycin derivative by S. fradiae Delta urdQ/R. J Biotechnol 2007; 130:32-8. [PMID: 17434221 PMCID: PMC2880504 DOI: 10.1016/j.jbiotec.2007.02.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 02/19/2007] [Indexed: 11/30/2022]
Abstract
A strain (S. fradiae Delta urdQ/R) with mutations in urdQ and urdR encoding a dTDP-hexose-3,4-dehydratase and a dTDP-hexose-4-ketoreductase, respectively, produces a new urdamycin analogue (urdamycin X) with changes in the polyketide structure. The structure of urdamycin X has been elucidated by NMR spectroscopy. Urdamycin X was not detectable, even in small amounts, in either S. fradiae Delta urdQ, in S. fradiae DeltaurdR or in S. fradiae A0, a mutant lacking all glycosyltransferase genes. Complementation of S. fradiae Delta urdQ/R restored urdamycin A production indicating that the mutations did not cause any polar effect.
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Affiliation(s)
- M. Fedoryshyn
- Institut für Pharmazeutische Wissenschaften, Lehrstuhl für Pharmazeutische Biologie und Biotechnologie Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - M. Nur-e-Alam
- Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose street, Lexington, KY 40536-0082, USA
| | - L. Zhu
- Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose street, Lexington, KY 40536-0082, USA
| | - A. Luzhetskyy
- Institut für Pharmazeutische Wissenschaften, Lehrstuhl für Pharmazeutische Biologie und Biotechnologie Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - J. Rohr
- Institut für Pharmazeutische Wissenschaften, Lehrstuhl für Pharmazeutische Biologie und Biotechnologie Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
- Corresponding author (chemistry). Tel.: +1 859 323 5031; fax: +1 859 257 7564
| | - A. Bechthold
- Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose street, Lexington, KY 40536-0082, USA
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50
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Anthracycline Biosynthesis: Genes, Enzymes and Mechanisms. ANTHRACYCLINE CHEMISTRY AND BIOLOGY I 2007. [DOI: 10.1007/128_2007_14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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