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Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100018. [PMID: 32647822 PMCID: PMC7337054 DOI: 10.1016/j.yjsbx.2019.100018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 11/23/2022]
Abstract
Thiolases are a well characterized family of enzymes with two distinct categories: degradative, β-ketoadipyl-CoA thiolases and biosynthetic, acetoacetyl-CoA thiolases. Both classes share an identical catalytic triad but catalyze reactions in opposite directions. Moreover, it is established that in contrast to the biosynthetic thiolases the degradative thiolases can accept substrates with broad chain lengths. Hitherto, no residue or structural pattern has been recognized that might help to discern the two thiolases, here we exploit, a tetrameric degradative thiolase from Pseudomonas putida KT2440 annotated as PcaF, as a model system to understand features which distinguishes the two classes using structural studies and bioinformatics analyses. Degradative thiolases have different active site architecture when compared to biosynthetic thiolases, demonstrating the dissimilar chemical nature of the active site architecture. Both thiolases deploy different "anchoring residues" to tether the large Coenzyme A (CoA) or CoA derivatives. Interestingly, the H356 of the catalytic triad in PcaF is directly involved in tethering the CoA/CoA derivatives into the active site and we were able to trap a gridlocked thiolase structure of the H356A mutant, where the CoA was found to be covalently linked to the catalytic cysteine residue, inhibiting the overall reaction. Further, X-ray structures with two long chain CoA derivatives, hexanal-CoA and octanal-CoA helped in delineating the long tunnel of 235 Å2 surface area in PcaF and led to identification of a unique covering loop exclusive to degradative thiolases that plays an active role in determining the tunnel length and the nature of the binding substrate.
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Key Words
- A-mutant-HAL-CoA, A-mutant-hexanal CoA complex
- A-mutant-Hex-CoA, A-mutant-Hexanoyl CoA complex
- A-mutants, H356A Mutant
- AA-mutants, H356A-C386A Mutant
- AS-mutant-OAL-CoA, AS-mutant-octanal CoA complex
- AS-mutant-Oct-CoA, AS-mutant-Octanoyl CoA complex
- AS-mutants, H356A-C90S Mutant
- Covalent locking
- Covering loop
- HAL, hexanal
- Hex-CoA, Hexanoyl CoA
- Hexanoyl CoA
- Mtb-thiolase, Mycobacterium tuberculosis thiolase
- OAL, octanal
- Oct-CoA, Octanoyl CoA
- Octanoyl CoA
- PcaF, β-ketoadipyl-CoA thiolase
- Tunnel
- Zr-thiolase, Zoogleria ramigera thiolase
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2
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Marshall AC, Bond CS, Bruning JB. Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew C. Marshall
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Charles S. Bond
- School
of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John B. Bruning
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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3
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Chapter 9. Synthetic probes for polyketide and nonribosomal peptide biosynthetic enzymes. Methods Enzymol 2009; 458:219-54. [PMID: 19374985 DOI: 10.1016/s0076-6879(09)04809-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Polyketides and nonribosomal peptides constitute two classes of small molecule natural products that are well-known for their ability to impact important biological processes in a multitude of ways. The modular biosynthetic enzymes responsible for production of these compounds (PKS and NRPS enzymes) have been the subject of extensive genetic, biochemical, and structural characterization, in part due to the potential utility their successful reengineering may have for the production of new therapeutics. In this chapter, we provide background as well as specific techniques in which synthetically produced small molecule probes have been applied to help better understand the mechanism and structure of PKS and NRPS biosynthetic pathways, as well as to help streamline their discovery process. The continued development and application of these methods has the potential to greatly complement our current approaches to the study of natural product biosynthesis.
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4
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Meriläinen G, Schmitz W, Wierenga RK, Kursula P. The sulfur atoms of the substrate CoA and the catalytic cysteine are required for a productive mode of substrate binding in bacterial biosynthetic thiolase, a thioester-dependent enzyme. FEBS J 2008; 275:6136-48. [PMID: 19016856 DOI: 10.1111/j.1742-4658.2008.06737.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thioesters are more reactive than oxoesters, and thioester chemistry is important for the reaction mechanisms of many enzymes, including the members of the thiolase superfamily, which play roles in both degradative and biosynthetic pathways. In the reaction mechanism of the biosynthetic thiolase, the thioester moieties of acetyl-CoA and the acetylated catalytic cysteine react with each other, forming the product acetoacetyl-CoA. Although a number of studies have been carried out to elucidate the thiolase reaction mechanism at the atomic level, relatively little is known about the factors determining the affinity of thiolases towards their substrates. We have carried out crystallographic studies on the biosynthetic thiolase from Zoogloea ramigera complexed with CoA and three of its synthetic analogues to compare the binding modes of these related compounds. The results show that both the CoA terminal SH group and the side chain SH group of the catalytic Cys89 are crucial for the correct positioning of substrate in the thiolase catalytic pocket. Furthermore, calorimetric assays indicate that the mutation of Cys89 into an alanine significantly decreases the affinity of thiolase towards CoA. Thus, although the sulfur atom of the thioester moiety is important for the reaction mechanism of thioester-dependent enzymes, its specific properties can also affect the affinity and competent mode of binding of the thioester substrates to these enzymes.
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5
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Koller M, Horvat P, Hesse P, Bona R, Kutschera C, Atlić A, Braunegg G. Assessment of formal and low structured kinetic modeling of polyhydroxyalkanoate synthesis from complex substrates. Bioprocess Biosyst Eng 2006; 29:367-77. [PMID: 17031672 DOI: 10.1007/s00449-006-0084-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
Abstract
A formal kinetic mathematical model for poly-(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) [P(3HB-co-3HV-co-4HB)] terpolyester synthesis from glucose and galactose derived from whey permeate supplemented with gamma-butyrolactone by the archaeon Haloferax mediterranei was created. Further, a low structured mathematical model for poly-3-hydroxybutyrate synthesis from whey permeate by Pseudomonas hydrogenovora was developed. In both cases, biosyntheses for obtaining the experimental data used for compiling the models were performed via fed-batch cultivations. The model developed for H. mediterranei consists of 10 differential and 11 algebraic equations, including 27 kinetic constants. The model compiled for P. hydrogenovora encompasses 10 differential and 3 algebraic equations, including 36 kinetic constants. Both models were solved by Runge-Kuta variable step numerical integration with Monte Carlo parameter optimization procedure. Difficulties arising from the modeling of redirection of metabolic fluxes from biomass growth toward polyhydroxyalkanoate synthesis and byproducts are discussed.
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Affiliation(s)
- Martin Koller
- Institute of Biotechnology and Bioprocess Engineering, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.
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6
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Mishra PK, Drueckhammer DG. Coenzyme A Analogues and Derivatives: Synthesis and Applications as Mechanistic Probes of Coenzyme A Ester-Utilizing Enzymes. Chem Rev 2000; 100:3283-3310. [PMID: 11777425 DOI: 10.1021/cr990010m] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pranab K. Mishra
- Department of Chemistry, State University at Stony Brook, Stony Brook, New York 11794
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7
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Ballestero RP, Dybowski JA, Levy G, Agranoff BW, Uhler MD. Cloning and characterization of zRICH, a 2',3'-cyclic-nucleotide 3'-phosphodiesterase induced during zebrafish optic nerve regeneration. J Neurochem 1999; 72:1362-71. [PMID: 10098837 DOI: 10.1046/j.1471-4159.1999.721362.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We previously reported cloning of cDNAs encoding both components of a protein doublet induced during goldfish optic nerve regeneration. The predicted protein sequences showed significant homology with the mammalian 2',3'-cyclic-nucleotide 3'-phosphodiesterases (CNPases). CNPases are well-established markers of mammalian myelin; hence, the cDNAs were designated gRICH68 and gRICH70 (for goldfish Regeneration-Induced CNPase Homologues of 68 and 70 kDa). Homologous cDNAs have now been isolated from zebrafish encoding a highly related protein, which we have termed zRICH. RNase protection assays show that zRICH mRNA is induced significantly (fivefold) in optic nerve regenerating zebrafish retinas 7 days following nerve crush. Western blots show a single band in zebrafish brain and retina extracts, with immunoreactivity increasing three-fold in regenerating retinas 21 days postcrush. Immunohistochemical analysis indicated that this increase in zRICH protein expression is localized to the retinal ganglion cell layer in regenerating retina. We have characterized and evaluated the relevance of a conserved beta-ketoacyl synthase motif in zRICH to CNPase activity by means of site-directed mutagenesis. Two residues within the motif, H334 and T336, are critical for enzymatic activity. A cysteine residue within the motif, which corresponds to a critical residue for beta-ketoacyl synthase, does not appear to participate in the phosphodiesterase activity.
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Affiliation(s)
- R P Ballestero
- Department of Biological Chemistry and Mental Health Research Institute, University of Michigan, Ann Arbor 48104-1687, USA
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8
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Madison LL, Huisman GW. Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic. Microbiol Mol Biol Rev 1999; 63:21-53. [PMID: 10066830 PMCID: PMC98956 DOI: 10.1128/mmbr.63.1.21-53.1999] [Citation(s) in RCA: 881] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs.
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Affiliation(s)
- L L Madison
- Metabolix, Inc., Cambridge, Massachusetts 02142, USA
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9
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Vogel KW, Drueckhammer DG. A Reversed Thioester Analogue of Acetyl-Coenzyme A: An Inhibitor of Thiolase and a Synthon for Other Acyl-CoA Analogues. J Am Chem Soc 1998. [DOI: 10.1021/ja971758u] [Citation(s) in RCA: 17] [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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10
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Affiliation(s)
- C Sasikala
- Department of Botany, Osmania University, Hyderabad, India
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11
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Gerngross TU, Reilly P, Stubbe J, Sinskey AJ, Peoples OP. Immunocytochemical analysis of poly-beta-hydroxybutyrate (PHB) synthase in Alcaligenes eutrophus H16: localization of the synthase enzyme at the surface of PHB granules. J Bacteriol 1993; 175:5289-93. [PMID: 8349571 PMCID: PMC205001 DOI: 10.1128/jb.175.16.5289-5293.1993] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Antibodies raised against the Alcaligenes eutrophus poly-beta-hydroxybutyrate (PHB) synthase polypeptide were used for immunocytochemical localization of the synthase enzyme in whole cells and purified PHB granules. The data presented demonstrate for the first time that the synthase enzyme is located on the surface of the PHB granule rather than being incorporated inside the granule during its formation. From these basic observations and data from the recent literature, a model of granule assembly is proposed.
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Affiliation(s)
- T U Gerngross
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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12
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McInerney MJ, Amos DA, Kealy KS, Palmer JA. Synthesis and function of polyhydroxyalkanoates in anaerobic syntrophic bacteria. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05838.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Liebergesell M, Steinbüchel A. Cloning and nucleotide sequences of genes relevant for biosynthesis of poly(3-hydroxybutyric acid) in Chromatium vinosum strain D. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 209:135-50. [PMID: 1396692 DOI: 10.1111/j.1432-1033.1992.tb17270.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
From a genomic library of Chromatium vinosum strain D in lambda L47, a 16.5-kbp EcoRI-restriction fragment was identified by hybridization with a DNA fragment harboring the operon for Alcaligenes eutrophus poly(3-hydroxyalkanoate) (PHA) synthesis. This fragment and subfragments thereof restored the ability to synthesize and accumulate PHA in PHA-negative mutants of A. eutrophus. A region of 6977 bp was sequenced; seven open reading frames (ORFs) were identified which probably represent coding regions; six of these are most probably relevant for PHA biosynthesis in C. vinosum. The structural genes for biosynthetic acetyl-CoA acyltransferase (beta-ketothiolase; phbACv, 1188 bp) and NADH-dependent acetoacetyl-CoA reductase (phbBCv, 741 bp) were separated by ORF4 (462 bp) and ORF5 (369 bp). Downstream of phbBCv ORF7 (471 pb) was identified which was not completed at the 3' terminus. The functions of ORF4, ORF5, and ORF7 are not known. The amino acid sequences of beta-ketothiolase and acetoacetyl-CoA reductase deduced from phbACv and phbBCv, exhibited a similarity of 68.2% and 56.4% identical amino acids, respectively, to the corresponding enzymes of A. eutrophus. Antilinear to and upstream of the genes mentioned above, two genes were identified which were transcribed from a sigma 70-dependent promoter. This promoter overlapped with and was divergent to the phbACv promoter; the transcriptional start sites were mapped by S1 nuclease protection assays. These genes were ORF2 (1074 bp), whose function is not known but whose presence in Escherichia coli is essential for expression of PHA synthase activity, and the structural gene for a PHA synthase of low M(r) (phbCCv, 1068 bp). The gene products of ORF2 and phbCCv, with M(r) of 40,525 and 39,730, respectively, were expressed in E. coli applying the T7 RNA polymerase/promoter system. Although the amino acid sequence of PHA synthase deduced from phbCCv exhibited only 24.7% overall similarity with the PHA synthase of A. eutrophus, highly conserved regions were identified.
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Affiliation(s)
- M Liebergesell
- Institut für Mikrobiologie, Georg-August-Universität Göttingen, Federal Republic of Germany
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14
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Biosynthetic thiolase from Zoogloea ramigera. Evidence for a mechanism involving Cys-378 as the active site base. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92985-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Wrensford LV, Coppola C, Anderson VE. An acyl-coenzyme A chain length dependent assay for 3-oxoacyl-coenzyme A thiolases employing acetyldithio-coenzyme A. Anal Biochem 1991; 192:49-54. [PMID: 2048733 DOI: 10.1016/0003-2697(91)90181-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An assay for 3-oxoacyl-coenzyme A (3-oxoacyl-CoA) thiolases is described. The reaction utilizes acetyldithio-CoA as the nucleophile and variable chain length saturated acyl-CoA's as the electrophiles. The properties of the 3-oxoacyl-CoA dithioester product, notably a pKa of 6.6 +/- 0.1 and an extinction coefficient of 21,600 cm-1 M-1 for the enethiolate at 357 nm, make it possible to spectrophotometrically follow the reaction in the thermodynamically unfavorable carbon-carbon bond-forming direction. These properties eliminate both the background decomposition and the dependence on Mg2+, chain length, and pH that complicate assays with 3-oxoacyl-CoA substrates. Purified thiolase I from pig liver was 140-fold more active with butyryl-CoA as the electrophile than with acetyl-CoA and 38-fold more reactive with hexanoyl-CoA than with myristoyl-CoA. Beef liver homogenate showed a much greater relative activity with myristoyl-CoA as the electrophile than either purified pig heart thiolase I or pig heart homogenate. The analysis of the separation of thiolases by anion-exchange chromatography is simplified and further suggests the existence of isozymes with varying chain length specificities.
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Affiliation(s)
- L V Wrensford
- Department of Chemistry, Brown University, Providence, Rhode Island 02912
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17
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Zeelen JP, Wierenga RK, Erdmann R, Kunau WH. Crystallographic studies of 3-ketoacylCoA thiolase from yeast Saccharomyces cerevisiae. J Mol Biol 1990; 215:211-3. [PMID: 2213879 DOI: 10.1016/s0022-2836(05)80338-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Good diffracting crystals of 3-ketoacylCoA thiolase (EC 2.3.1.16) from yeast Saccharomyces cerevisiae have been obtained. The crystals diffract to at least 2.4 A. The space group of these crystals is P2(1)2(1)2(1), with cell dimensions a = 71.8 A, b = 93.8 A and c = 119.9 A. There is one dimer per asymmetric unit.
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Affiliation(s)
- J P Zeelen
- European Molecular Biology Laboratory, Heidelberg, F.R.G
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18
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Anderson VE, Bahnson BJ, Wlassics ID, Walsh CT. The reaction of acetyldithio-CoA, a readily enolized analog of acetyl-CoA with thiolase from Zoogloea ramigera. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39318-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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19
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Doi Y, Kawaguchi Y, Nakamura Y, Kunioka M. Nuclear Magnetic Resonance Studies of Poly(3-Hydroxybutyrate) and Polyphosphate Metabolism in
Alcaligenes eutrophus. Appl Environ Microbiol 1989; 55:2932-8. [PMID: 16348055 PMCID: PMC203193 DOI: 10.1128/aem.55.11.2932-2938.1989] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The metabolic pathways of poly(3-hydroxybutyrate) (PHB) and polyphosphate in the microorganism
Alcaligenes eutrophus
H16 were studied by
1
H,
13
C, and
31
P nuclear magnetic resonance (NMR) spectroscopy and by conventional analytical techniques.
A. eutrophus
cells accumulated two storage polymers of PHB and polyphosphate in the presence of carbon and phosphate sources under aerobic conditions after exhaustion of nitrogen sources. The solid-state cross-polarization/magic-angle spinning
13
C NMR spectroscopy was used to study the biosynthetic pathways of PHB and other cellular biomass components from
13
C-labeled acetate. The solid-state
13
C NMR analysis of lyophilized intact cells grown on [1-
13
C]acetate indicated that the carbonyl carbon of acetate was selectively incorporated both into the carbonyl and methine carbons of PHB and into the carbonyl carbons of proteins. The
31
P NMR analysis of
A. eutrophus
cells in suspension showed that the synthesis of intracellular polyphosphate was closely related to the synthesis of PHB. The roles of PHB and polyphosphate in the cells were studied under conditions of carbon, phosphorus, and nitrogen source starvation. Under both aerobic and anaerobic conditions PHB was degraded, whereas little polyphosphate was degraded. The rate of PHB degradation under anaerobic conditions was faster than that under aerobic conditions. Under anaerobic conditions, acetate and 3-hydroxybutyrate were produced as the major extracellular metabolites. The implications of this observation are discussed in connection with the regulation of PHB and polyphosphate metabolism in
A. eutrophus.
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Affiliation(s)
- Y Doi
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 227, Japan
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21
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Peoples OP, Sinskey AJ. Fine structural analysis of the Zoogloea ramigera phbA-phbB locus encoding beta-ketothiolase and acetoacetyl-CoA reductase: nucleotide sequence of phbB. Mol Microbiol 1989; 3:349-57. [PMID: 2546004 DOI: 10.1111/j.1365-2958.1989.tb00180.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A series of expression plasmids containing either the complete insert from plasmid pUCDBK1 (Peoples et al., 1987) or sub-fragments thereof were constructed in a tac promoter vector. Analysis of protein lysates of induced cultures of these clones identified the gene encoding NADPH-specific acetoacetyl-CoA reductase in the 2.3kb of sequence located downstream from the beta-ketothiolase gene in plasmid pUCDBK1. The complete nucleotide sequence (2.1kb) of this region was determined. An open reading frame was located 88bp downstream from the stop codon of the thiolase gene encoding a potential polypeptide of Mr 25,000, which is in good agreement with that observed for the overexpressed protein on SDS-PAGE. N-terminal protein sequence data obtained by Edman degradation of the purified Mr = 25,000 polypeptide were used to identify the correct start of the NADPH-specific acetoacetyl-CoA reductase gene. Hence in Z. ramigera, the genes encoding beta-ketothiolase (phbA) and NADPH-specific acetoacetyl-CoA reductase (phbB) are organized as phbA-phbB. S1-nuclease analysis of Z. ramigera RNA identified a transcription start site 85 bp upstream from the phbA structural gene locating the promoter region.
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Affiliation(s)
- O P Peoples
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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22
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Haywood G, Anderson A, Chu L, Dawes E. Characterization of two 3-ketothiolases possessing differing substrate specificities in the polyhydroxyalkanoate synthesizing organismAlcaligenes eutrophus. FEMS Microbiol Lett 1988. [DOI: 10.1111/j.1574-6968.1988.tb02577.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Ploux O, Masamune S, Walsh CT. The NADPH-linked acetoacetyl-CoA reductase from Zoogloea ramigera. Characterization and mechanistic studies of the cloned enzyme over-produced in Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 174:177-82. [PMID: 3286259 DOI: 10.1111/j.1432-1033.1988.tb14079.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The NADPH-linked acetoacetyl-CoA reductase, (R)-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.36), from the bacterium Zoogloea ramigera, involved in the formation of D-3-hydroxybutyryl-CoA for poly(D-3-hydroxybutyrate) biosynthesis, has been purified from an over-producing Escherichia coli strain. The purification was achieved in two steps, yielding an electrophoretically homogeneous enzyme of high specific activity (608 U/mg). The enzyme is an alpha 4 homotetramer of four 25-kDa subunits. It has a Km of 2 microM and a kcat/Km of 1.8 X 10(8) M-1 s-1 for acetoacetyl-CoA; it is inhibited by acetoacetyl-CoA above 10 microM. K is 10(-10) M for the dehydrogenation. Kinetic studies of the back reaction revealed a sequential mechanism involving a ternary complex. The stereospecificity of the hydride-equivalent transfer was demonstrated using NMR techniques to be 4S (B side). Using the fingerprint method proposed by Wierenga et al. [(1986) J. Mol. Biol. 187, 101-107], we identified a 28-residue stretch (residues 3-31) as a possible NADPH fold. Finally the specificity of the reductase was examined using 3-oxo-acyl-CoA analogs and analogs lacking the adenosine 3',5'-bisphosphate moiety of CoA. Only the straight-chain C5 analog (3-oxo-propionyl-CoA) was found to be an alternative substrate (40%) for the reductase.
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Affiliation(s)
- O Ploux
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge
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24
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Biosynthetic thiolase from zoogloea ramigera. I. Preliminary characterization and analysis of proton transfer reaction. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75891-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Biosynthetic thiolase from Zoogloea ramigera. III. Isolation and characterization of the structural gene. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(19)75893-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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