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Rajpurohit H, Eiteman MA. Citrate synthase variants improve yield of acetyl-CoA derived 3-hydroxybutyrate in Escherichia coli. Microb Cell Fact 2024; 23:173. [PMID: 38867236 PMCID: PMC11167817 DOI: 10.1186/s12934-024-02444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The microbial chiral product (R)-3-hydroxybutyrate (3-HB) is a gateway to several industrial and medical compounds. Acetyl-CoA is the key precursor for 3-HB, and several native pathways compete with 3-HB production. The principal competing pathway in wild-type Escherichia coli for acetyl-CoA is mediated by citrate synthase (coded by gltA), which directs over 60% of the acetyl-CoA into the tricarboxylic acid cycle. Eliminating citrate synthase activity (deletion of gltA) prevents growth on glucose as the sole carbon source. In this study, an alternative approach is used to generate an increased yield of 3-HB: citrate synthase activity is reduced but not eliminated by targeted substitutions in the chromosomally expressed enzyme. RESULTS Five E. coli GltA variants were examined for 3-HB production via heterologous overexpression of a thiolase (phaA) and NADPH-dependent acetoacetyl-CoA reductase (phaB) from Cupriavidus necator. In shake flask studies, four variants showed nearly 5-fold greater 3-HB yield compared to the wild-type, although pyruvate accumulated. Overexpression of either native thioesterases TesB or YciA eliminated pyruvate formation, but diverted acetyl-CoA towards acetate formation. Overexpression of pantothenate kinase similarly decreased pyruvate formation but did not improve 3-HB yield. Controlled batch studies at the 1.25 L scale demonstrated that the GltA[A267T] variant produced the greatest 3-HB titer of 4.9 g/L with a yield of 0.17 g/g. In a phosphate-starved repeated batch process, E. coli ldhA poxB pta-ackA gltA::gltA[A267T] generated 15.9 g/L 3-HB (effective concentration of 21.3 g/L with dilution) with yield of 0.16 g/g from glucose as the sole carbon source. CONCLUSIONS This study demonstrates that GltA variants offer a means to affect the generation of acetyl-CoA derived products. This approach should benefit a wide range of acetyl-CoA derived biochemical products in E. coli and other microbes. Enhancing substrate affinity of the introduced pathway genes like thiolase towards acetyl-CoA will likely further increase the flux towards 3-HB while reducing pyruvate and acetate accumulation.
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Affiliation(s)
| | - Mark A Eiteman
- School of Chemical, Materials and Biomedical Engineering, Athens, GA, USA.
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH. Identification of a proteolysis regulator for an essential enzyme in Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587195. [PMID: 38585835 PMCID: PMC10996600 DOI: 10.1101/2024.03.29.587195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
In Mycobacterium tuberculosis proteins that are post-translationally modified with Pup, a prokaryotic ubiquitin-like protein, can be degraded by proteasomes. While pupylation is reversible, mechanisms regulating substrate specificity have not been identified. Here, we identify the first depupylation regulators: CoaX, a pseudokinase, and pantothenate, an essential, central metabolite. In a Δ coaX mutant, pantothenate synthesis enzymes were more abundant, including PanB, a substrate of the Pup-proteasome system. Media supplementation with pantothenate decreased PanB levels in a coaX and Pup-proteasome-dependent manner. In vitro , CoaX accelerated depupylation of Pup∼PanB, while addition of pantothenate inhibited this reaction. Collectively, we propose CoaX contributes to proteasomal degradation of PanB by modulating depupylation of Pup∼PanB in response to pantothenate levels. One Sentence Summary A pseudo-pantothenate kinase regulates proteasomal degradation of a pantothenate synthesis enzyme in M. tuberculosis .
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Riske BF, Luckhart S, Riehle MA. Starving the Beast: Limiting Coenzyme A Biosynthesis to Prevent Disease and Transmission in Malaria. Int J Mol Sci 2023; 24:13915. [PMID: 37762222 PMCID: PMC10530615 DOI: 10.3390/ijms241813915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Malaria parasites must acquire all necessary nutrients from the vertebrate and mosquito hosts to successfully complete their life cycle. Failure to acquire these nutrients can limit or even block parasite development and presents a novel target for malaria control. One such essential nutrient is pantothenate, also known as vitamin B5, which the parasite cannot synthesize de novo and is required for the synthesis of coenzyme A (CoA) in the parasite. This review examines pantothenate and the CoA biosynthesis pathway in the human-mosquito-malaria parasite triad and explores possible approaches to leverage the CoA biosynthesis pathway to limit malaria parasite development in both human and mosquito hosts. This includes a discussion of sources for pantothenate for the mosquito, human, and parasite, examining the diverse strategies used by the parasite to acquire substrates for CoA synthesis across life stages and host resource pools and a discussion of drugs and alternative approaches being studied to disrupt CoA biosynthesis in the parasite. The latter includes antimalarial pantothenate analogs, known as pantothenamides, that have been developed to target this pathway during the human erythrocytic stages. In addition to these parasite-targeted drugs, we review studies of mosquito-targeted allosteric enzymatic regulators known as pantazines as an approach to limit pantothenate availability in the mosquito and subsequently deprive the parasite of this essential nutrient.
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Affiliation(s)
- Brendan F. Riske
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA;
| | - Shirley Luckhart
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA;
- Department of Biological Sciences, University of Idaho, Moscow, ID 83843, USA
| | - Michael A. Riehle
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA;
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4
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Kudo H, Ono S, Abe K, Matsuda M, Hasunuma T, Nishizawa T, Asayama M, Nishihara H, Chohnan S. Enhanced supply of acetyl-CoA by exogenous pantothenate kinase promotes synthesis of poly(3-hydroxybutyrate). Microb Cell Fact 2023; 22:75. [PMID: 37081440 PMCID: PMC10116679 DOI: 10.1186/s12934-023-02083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Coenzyme A (CoA) is a carrier of acyl groups. This cofactor is synthesized from pantothenic acid in five steps. The phosphorylation of pantothenate is catalyzed by pantothenate kinase (CoaA), which is a key step in the CoA biosynthetic pathway. To determine whether the enhancement of the CoA biosynthetic pathway is effective for producing useful substances, the effect of elevated acetyl-CoA levels resulting from the introduction of the exogenous coaA gene on poly(3-hydroxybutyrate) [P(3HB)] synthesis was determined in Escherichia coli, which express the genes necessary for cyanobacterial polyhydroxyalkanoate synthesis (phaABEC). RESULTS E. coli containing the coaA gene in addition to the pha genes accumulated more P(3HB) compared with the transformant containing the pha genes alone. P(3HB) production was enhanced by precursor addition, with P(3HB) content increasing from 18.4% (w/w) to 29.0% in the presence of 0.5 mM pantothenate and 16.3%-28.2% by adding 0.5 mM β-alanine. Strains expressing the exogenous coaA in the presence of precursors contained acetyl-CoA in excess of 1 nmol/mg of dry cell wt, which promoted the reaction toward P(3HB) formation. The amount of acetate exported into the medium was three times lower in the cells carrying exogenous coaA and pha genes than in the cells carrying pha genes alone. This was attributed to significantly enlarging the intracellular pool size of CoA, which is the recipient of acetic acid and is advantageous for microbial production of value-added materials. CONCLUSIONS Enhancing the CoA biosynthetic pathway with exogenous CoaA was effective at increasing P(3HB) production. Supplementing the medium with pantothenate facilitated the accumulation of P(3HB). β-Alanine was able to replace the efficacy of adding pantothenate.
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Affiliation(s)
- Hirotaka Kudo
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Sho Ono
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Kenta Abe
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomoyasu Nishizawa
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Munehiko Asayama
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Hirofumi Nishihara
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Shigeru Chohnan
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan.
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5
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Brigg SE, Koekemoer L, Brand LA, Strauss E. Multifaceted Target Specificity Analysis as a Tool in Antimicrobial Drug Development: Type III Pantothenate Kinases as a Case Study. ChemMedChem 2023; 18:e202200630. [PMID: 36749500 DOI: 10.1002/cmdc.202200630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/08/2023]
Abstract
The research and development of a new antimicrobial drug using a target-based approach raises the question of whether any resulting hits will also show activity against the homologous target in other closely related organisms. While an assessment of the similarities of the predicted interactions between the identified inhibitor and the various targets is an obvious first step in answering this question, no clear and consistent framework has been proposed for how this should be done. Here we developed Multifaceted Target Specificity Analysis (MTSA) and applied it to type III pantothenate kinase (PanKIII ) - an essential enzyme required for coenzyme A biosynthesis in a wide range of pathogenic bacteria - as a case study to establish if targeting a specific organism's PanKIII would lead to a narrow- or broad-spectrum agent. We propose that MTSA is a useful tool and aid for directing new target-based antimicrobial drug development initiatives.
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Affiliation(s)
- Siobhan Ernan Brigg
- Department of Biochemistry, Stellenbosch University, Matieland, 7602, South Africa
| | - Lizbé Koekemoer
- Department of Biochemistry, Stellenbosch University, Matieland, 7602, South Africa
| | - Leisl A Brand
- Department of Biochemistry, Stellenbosch University, Matieland, 7602, South Africa
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Matieland, 7602, South Africa
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6
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Kaku M, Ishidaira M, Satoh S, Ozaki M, Kohari D, Chohnan S. Fatty Acid Production by Enhanced Malonyl-CoA Supply in Escherichia coli. Curr Microbiol 2022; 79:269. [PMID: 35881256 DOI: 10.1007/s00284-022-02969-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022]
Abstract
The expression of exogenous genes encoding acetyl-CoA carboxylase (Acc) and pantothenate kinase (CoaA) in Escherichia coli enable highly effective fatty acid production. Acc-only strains grown at 37 °C or 23 °C produced an approximately twofold increase in fatty acid content, and additional expression of CoaA achieved a further twofold accumulation. In the presence of pantothenate, which is the starting material for the CoA biosynthetic pathway, the size of the intracellular CoA pool at 23 °C was comparable to that at 30 °C during cultivation, and more than 500 mg/L of culture containing cellular fatty acids was produced, even at 23 °C. However, the highest yield of cellular fatty acids (1100 mg/L of culture) was produced in cells possessing the gene encoding type I bacterial fatty acid synthase (FasA) along with the acc and coaA, when the transformant was cultivated at 30 °C in M9 minimal salt medium without pantothenate or IPTG. This E. coli transformant contained 141 mg/L of oleic acid attributed to FasA under noninducible conditions. The increased fatty acid content was brought about by a greatly improved specific productivity of 289 mg/g of dry cell weight. Thus, the effectiveness of the foreign acc and coaA in fatty acid production was unambiguously confirmed at culture temperatures of 23 °C to 37 °C. Cofactor engineering in E. coli using the exogenous coaA and acc genes resulted in fatty acid production over 1 g/L of culture and could effectively function at 23 °C.
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Affiliation(s)
- Moena Kaku
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Mei Ishidaira
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Shusaku Satoh
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Miho Ozaki
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Daisuke Kohari
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan
| | - Shigeru Chohnan
- Department of Food and Life Sciences, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki, 300-0393, Japan.
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7
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de Vries LE, Lunghi M, Krishnan A, Kooij TWA, Soldati-Favre D. Pantothenate and CoA biosynthesis in Apicomplexa and their promise as antiparasitic drug targets. PLoS Pathog 2021; 17:e1010124. [PMID: 34969059 PMCID: PMC8717973 DOI: 10.1371/journal.ppat.1010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These parasites are characterized by complex and divergent life cycles occupying a variety of host niches. Consequently, they exhibit distinct adaptations to the differences in nutritional availabilities, either relying on biosynthetic pathways or by salvaging metabolites from their host. Pantothenate (Pan, vitamin B5) is the precursor for the synthesis of an essential cofactor, coenzyme A (CoA), but among the apicomplexans, only the coccidian subgroup has the ability to synthesize Pan. While the pathway to synthesize CoA from Pan is largely conserved across all branches of life, there are differences in the redundancy of enzymes and possible alternative pathways to generate CoA from Pan. Impeding the scavenge of Pan and synthesis of Pan and CoA have been long recognized as potential targets for antimicrobial drug development, but in order to fully exploit these critical pathways, it is important to understand such differences. Recently, a potent class of pantothenamides (PanAms), Pan analogs, which target CoA-utilizing enzymes, has entered antimalarial preclinical development. The potential of PanAms to target multiple downstream pathways make them a promising compound class as broad antiparasitic drugs against other apicomplexans. In this review, we summarize the recent advances in understanding the Pan and CoA biosynthesis pathways, and the suitability of these pathways as drug targets in Apicomplexa, with a particular focus on the cyst-forming coccidian, Toxoplasma gondii, and the haemosporidian, Plasmodium falciparum.
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Affiliation(s)
- Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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8
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Tjhin ET, Howieson VM, Spry C, van Dooren GG, Saliba KJ. A novel heteromeric pantothenate kinase complex in apicomplexan parasites. PLoS Pathog 2021; 17:e1009797. [PMID: 34324601 PMCID: PMC8366970 DOI: 10.1371/journal.ppat.1009797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 08/16/2021] [Accepted: 07/13/2021] [Indexed: 11/19/2022] Open
Abstract
Coenzyme A is synthesised from pantothenate via five enzyme-mediated steps. The first step is catalysed by pantothenate kinase (PanK). All PanKs characterised to date form homodimers. Many organisms express multiple PanKs. In some cases, these PanKs are not functionally redundant, and some appear to be non-functional. Here, we investigate the PanKs in two pathogenic apicomplexan parasites, Plasmodium falciparum and Toxoplasma gondii. Each of these organisms express two PanK homologues (PanK1 and PanK2). We demonstrate that PfPanK1 and PfPanK2 associate, forming a single, functional PanK complex that includes the multi-functional protein, Pf14-3-3I. Similarly, we demonstrate that TgPanK1 and TgPanK2 form a single complex that possesses PanK activity. Both TgPanK1 and TgPanK2 are essential for T. gondii proliferation, specifically due to their PanK activity. Our study constitutes the first examples of heteromeric PanK complexes in nature and provides an explanation for the presence of multiple PanKs within certain organisms.
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Affiliation(s)
- Erick T. Tjhin
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Vanessa M. Howieson
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Giel G. van Dooren
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Kevin J. Saliba
- Research School of Biology, The Australian National University, Canberra, Australia
- Medical School, The Australian National University, Canberra, Australia
- * E-mail:
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9
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Abstract
Coenzyme A (CoA) is an essential cofactor present in all domains of life and is involved in numerous metabolic pathways, including fatty acid metabolism, pyruvate oxidation through the tricarboxylic acid (TCA) cycle, and the production of secondary metabolites. This characteristic makes CoA a commercially valuable compound in the pharmaceutical, cosmetic, and clinical industries. However, CoA is difficult to accumulate in living cells at a high level, since it is consumed in multiple metabolic pathways, hampering its manufacturing by typical cell cultivation and extraction approaches. The feedback inhibition by CoA to a biosynthetic enzyme, pantothenate kinase (PanK), is also a serious obstacle for the high-titer production of CoA. To overcome this challenge, in vitro production of CoA, in which the CoA biosynthetic pathway was reconstructed outside cells using recombinant thermophilic enzymes, was performed. The in vitro pathway was designed to be insensitive to the feedback inhibition of CoA using CoA-insensitive type III PanK from the thermophilic bacterium Thermus thermophilus. Furthermore, a statistical approach using design of experiments (DOE) was employed to rationally determine the enzyme loading ratio to maximize the CoA production rate. Consequently, 0.94 mM CoA could be produced from 2 mM d-pantetheine through the designed pathway. We hypothesized that the insufficient conversion yield is attributed to the high Km value of T. thermophilus PanK toward ATP. Based on these observations, possible CoA regulation mechanisms in T. thermophilus and approaches to improve the feasibility of CoA production through the in vitro pathway have been investigated. IMPORTANCE The biosynthesis of coenzyme A (CoA) in bacteria and eukaryotes is regulated by feedback inhibition targeting type I and type II pantothenate kinase (PanK). Type III PanK is found only in bacteria and is generally insensitive to CoA. Previously, type III PanK from the hyperthermophilic bacterium Thermotoga maritima was shown to defy this typical characteristic and instead shows inhibition toward CoA. In the present study, phylogenetic analysis combined with functional analysis of type III PanK from thermophiles revealed that the CoA-sensitive behavior of type III PanK from T. maritima is uncommon. We cloned type III PanKs from Thermus thermophilus and Geobacillus sp. strain 30 and showed that neither enzyme's activities were inhibited by CoA. Furthermore, we utilized type III PanK for a one-pot cascade reaction to produce CoA.
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10
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Singla A, Sharma P, Gupta A, Iqbal N, Rani C, Singh TP, Sharma S. Biophysical Characterization of Type III Pantothenate Kinase (PanK) from Acinetobacter baumannii. Protein Pept Lett 2021; 28:450-458. [PMID: 32798368 DOI: 10.2174/0929866527666200813202445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Type-III Pantothenate kinase from the multi drug resistant bacteria, Acinetobacter baumannii (AbPanK) catalyzes the first step of the essential Coenzyme A biosynthesis pathway. AbPanK is an attractive drug target against the bacteria since it is an essential enzyme and its structure is significantly different from the human PanK. METHODS AbPanK was cloned, expressed, purified and crystallized. A good quality single crystal was used for X-ray intensity data collection. Dynamic light scattering was done for calculating the hydrodynamic radii and its oligomeric nature in the solution. Binding studies of this protein with its two substrates, Pantothenate and ATP were done using spectrofluorometer. RESULTS Our results indicated that AbPanK shows a strong affinity with pantothenate with dissociation constant of 1.2 x 10- 8 M and moderate affinity towards ATP of 3.7x 10-3 M. This fact was further substantiated by the calculations of Km of both substrates using kinase assay kit. Dynamic light scattering studies have shown that it exists as homogenous solution with hydrodynamic radii corresponding to the molecular weight of 29.55 kDa. A low-resolution X-ray intensity data set was collected, which shows that AbPank crystallizes in P2 space group with cell dimensions of a= 165 Å, b= 260 Å, and, c= 197 Å and α= 90.0, β= 113.60, γ= 90.0. DISCUSSION Recombinant Pantothenate kinase from Acinetobacter baumannii was purified to homogeneity and crystallized. The enzyme exhibits very low sequence identity (28%) to other corresponding enzymes. CONCLUSION The recombinant enzyme was active and its binding affinities with its substrates pantothenate and ATP have been studied. This information would be very useful while designing the inhibitors of this enzyme in order to fight bacterial infections associated to this pathogen.
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Affiliation(s)
- Ankita Singla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Akshita Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Naseer Iqbal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Chitra Rani
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
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11
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Enhancement of fatty acid biosynthesis by exogenous acetyl-CoA carboxylase and pantothenate kinase in Escherichia coli. Biotechnol Lett 2020; 42:2595-2605. [DOI: 10.1007/s10529-020-02996-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023]
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12
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Werning M, Müllner EW, Mlynek G, Dobretzberger V, Djinovic-Carugo K, Baron DM, Prokisch H, Büchner B, Klopstock T, Salzer U. PKAN neurodegeneration and residual PANK2 activities in patient erythrocytes. Ann Clin Transl Neurol 2020; 7:1340-1351. [PMID: 32705819 PMCID: PMC7448160 DOI: 10.1002/acn3.51127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Abstract
Objective Pantothenate kinase 2‐associated neurodegeneration (PKAN) is a rare neurodegenerative disease caused by mutations in the pantothenate kinase 2 (PANK2) gene. PKAN is associated with iron deposition in the basal ganglia and, occasionally, with the occurrence of misshaped erythrocytes (acanthocytes). The aim of this study was to assess residual activity of PANK2 in erythrocytes of PKAN patients and to correlate these data with the type of PANK2 mutations and the progression of neurodegeneration. Methods Residual PANK2 activities in erythrocytes of 14 PKAN patients and 14 related carriers were assessed by a radiometric assay. Clinical data on neurodegeneration included the Barry–Albright Dystonia Scale (BAD‐Scale) besides further general patient features. A molecular visualization and analysis program was used to rationalize the influence of the PKAN causing mutations on a molecular level. Results Erythrocytes of PKAN patients had markedly reduced or no PANK2 activity. However, patients with at least one allele of the c.1583C > T (T528M) or the c.833G > T (R278L) variant exhibited 12–56% of residual PANK2 activity. In line, molecular modeling indicated only minor effects on enzyme structure for these point mutations. On average, these patients with c.1583C > T or c.833G > T variant had lower BAD scores corresponding to lower symptom severity than patients with other PANK2 point mutations. Interpretation Residual erythrocyte PANK2 activity could be a predictor for the progression of neurodegeneration in PKAN patients. Erythrocytes are an interesting patient‐derived cell system with still underestimated diagnostic potential.
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Affiliation(s)
- Maike Werning
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Ernst W Müllner
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Verena Dobretzberger
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - David M Baron
- Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Medical University of Vienna, Vienna, Austria
| | - Holger Prokisch
- Institute of Human Genetics, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Boriana Büchner
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, LMU Munich, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, LMU Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Ulrich Salzer
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
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13
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Veale CGL, Müller R. Recent Highlights in Anti-infective Medicinal Chemistry from South Africa. ChemMedChem 2020; 15:809-826. [PMID: 32149446 DOI: 10.1002/cmdc.202000086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/17/2022]
Abstract
Global advancements in biological technologies have vastly increased the variety of and accessibility to bioassay platforms, while simultaneously improving our understanding of druggable chemical space. In the South African context, this has resulted in a rapid expansion in the number of medicinal chemistry programmes currently operating, particularly on university campuses. Furthermore, the modern medicinal chemist has the advantage of being able to incorporate data from numerous related disciplines into the medicinal chemistry process, allowing for informed molecular design to play a far greater role than previously possible. Accordingly, this review focusses on recent highlights in drug-discovery programmes, in which South African medicinal chemistry groups have played a substantive role in the design and optimisation of biologically active compounds which contribute to the search for promising agents for infectious disease.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Ronel Müller
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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14
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Wang Y, Guan J, Di Trani JM, Auclair K, Mittermaier AK. Inhibition and Activation of Kinases by Reaction Products: A Reporter-Free Assay. Anal Chem 2019; 91:11803-11811. [PMID: 31426630 DOI: 10.1021/acs.analchem.9b02456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Kinases are widely distributed in nature and are implicated in many human diseases. Thus, an understanding of their activity and regulation is of fundamental importance. Several kinases are known to be inhibited by ADP. However, thorough investigation of this phenomenon is hampered by the lack of a simple and effective assay for studying this inhibition. We now present a quick, general approach for measuring the effects of reaction products on kinase activity. The method, based on isothermal titration calorimetry, is the first universal, reporter-free, continuous assay for probing kinase inhibition or activation by ADP. In applications to an aminoglycoside phosphotransferase [APH(3')-IIIa] and pantothenate kinases from Escherichia coli (EcPanK) and Pseudomonas aeruginosa (PaPanK), we found ADP to be an efficient inhibitor of all three kinases, with inhibition constant (Ki) values similar to or lower than the Michaelis-Menten constant (Km) values of ATP. Interestingly, ADP was an activator at low concentrations and an inhibitor at high concentrations for EcPanK. This unusual effect was quantitatively modeled and attributed to cooperative interactions between the two subunits of the dimeric enzyme. Importantly, our results suggest that, at typical bacterial intracellular concentrations of ATP and ADP (approximately 1.5 mM and 180 μM, respectively), all three kinases are partially inhibited by ADP, allowing enzyme activity to rapidly respond to changes in the levels of both metabolites.
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Affiliation(s)
- Yun Wang
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Jinming Guan
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Justin M Di Trani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Anthony K Mittermaier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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15
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Duncan D, Auclair K. The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation. Arch Biochem Biophys 2019; 672:108069. [PMID: 31404525 DOI: 10.1016/j.abb.2019.108069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
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16
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Yao J, Subramanian C, Rock CO, Jackowski S. Human pantothenate kinase 4 is a pseudo-pantothenate kinase. Protein Sci 2019; 28:1031-1047. [PMID: 30927326 PMCID: PMC6511746 DOI: 10.1002/pro.3611] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/28/2019] [Indexed: 11/07/2022]
Abstract
Pantothenate kinase generates 4'-phosphopantothenate in the first and rate-determining step of coenzyme A (CoA) biosynthesis. The human genome encodes three well-characterized and nearly identical pantothenate kinases (PANK1-3) plus a putative bifunctional protein (PANK4) with a predicted amino-terminal pantothenate kinase domain fused to a carboxy-terminal phosphatase domain. Structural and phylogenetic analyses show that all active, characterized PANKs contain the key catalytic residues Glu138 and Arg207 (HsPANK3 numbering). However, all amniote PANK4s, including human PANK4, encode Glu138Val and Arg207Trp substitutions which are predicted to inactivate kinase activity. Biochemical analysis corroborates bioinformatic predictions-human PANK4 lacks pantothenate kinase activity. Introducing Glu138Val and Arg207Trp substitutions to the human PANK3 and plant PANK4 abolished their robust pantothenate kinase activity. Introducing both catalytic residues back into human PANK4 restored kinase activity, but only to a low level. This result suggests that epistatic changes to the rest of the protein already reduced the kinase activity prior to mutation of the catalytic residues in the course of evolution. The PANK4 from frog, an anamniote living relative encoding the catalytically active residues, had only a low level of kinase activity, supporting the view that HsPANK4 had reduced kinase activity prior to the catalytic residue substitutions in amniotes. Together, our data show that human PANK4 is a pseudo-pantothenate kinase-a catalytically deficient variant of the catalytically active PANK4 found in plants and fungi. The Glu138Val and Arg207Trp substitutions in amniotes (HsPANK3 numbering) completely deactivated the pantothenate kinase activity that had already been reduced by prior epistatic mutations.
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Affiliation(s)
- Jiangwei Yao
- Department of Infectious DiseasesSt. Jude Children's Research HospitalMemphisTennessee, 38105
| | - Chitra Subramanian
- Department of Infectious DiseasesSt. Jude Children's Research HospitalMemphisTennessee, 38105
| | - Charles O. Rock
- Department of Infectious DiseasesSt. Jude Children's Research HospitalMemphisTennessee, 38105
| | - Suzanne Jackowski
- Department of Infectious DiseasesSt. Jude Children's Research HospitalMemphisTennessee, 38105
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17
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Shapiro JA, Varga JJ, Parsonage D, Walton W, Redinbo MR, Ross LJ, White EL, Bostwick R, Wuest WM, Claiborne A, Goldberg JB. Identification of Specific and Nonspecific Inhibitors of Bacillus anthracis Type III Pantothenate Kinase (PanK). ChemMedChem 2019; 14:78-82. [PMID: 30376607 PMCID: PMC6456334 DOI: 10.1002/cmdc.201800652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/30/2018] [Indexed: 11/08/2022]
Abstract
Antibiotics with novel mechanisms of action are desperately needed to combat the increasing rates of multidrug-resistant infections. Bacterial pantothenate kinase (PanK) has emerged as a target of interest to cut off the biosynthesis of coenzyme A. Herein we report the results of an in vitro high-throughput screen of over 10 000 small molecules against Bacillus anthracis PanK, as well as a follow-up screen of hits against PanK isolated from Pseudomonas aeruginosa and Burkholderia cenocepacia. Nine hits are structurally categorized and analyzed to set the stage for future drug development.
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Affiliation(s)
- Justin A. Shapiro
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA),
| | - John J. Varga
- Department of Pediatrics, Emory University School of Medicine, 1510 Clifton, Road NE, Suite 3009, Atlanta, GA 30322 (USA),
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157 (USA),
| | - William Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, 4350 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599-3290 (USA)
| | - Matthew R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, 4350 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599-3290 (USA)
| | - Larry J. Ross
- Southern Research, High-Throughput Screening Center, 2000 Ninth Avenue South, Birmingham, AL 35205 (USA),
| | - E. Lucile White
- Southern Research, High-Throughput Screening Center, 2000 Ninth Avenue South, Birmingham, AL 35205 (USA),
| | - Robert Bostwick
- Southern Research, High-Throughput Screening Center, 2000 Ninth Avenue South, Birmingham, AL 35205 (USA),
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA),
- Emory Antibiotic Resistance Center, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322 (USA)
| | - Al Claiborne
- Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157 (USA),
| | - Joanna B. Goldberg
- Department of Pediatrics, Emory University School of Medicine, 1510 Clifton, Road NE, Suite 3009, Atlanta, GA 30322 (USA),
- Emory Antibiotic Resistance Center, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322 (USA)
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18
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Probing the ligand preferences of the three types of bacterial pantothenate kinase. Bioorg Med Chem 2018; 26:5896-5902. [DOI: 10.1016/j.bmc.2018.10.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022]
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19
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Tjhin ET, Spry C, Sewell AL, Hoegl A, Barnard L, Sexton AE, Siddiqui G, Howieson VM, Maier AG, Creek DJ, Strauss E, Marquez R, Auclair K, Saliba KJ. Mutations in the pantothenate kinase of Plasmodium falciparum confer diverse sensitivity profiles to antiplasmodial pantothenate analogues. PLoS Pathog 2018; 14:e1006918. [PMID: 29614109 PMCID: PMC5882169 DOI: 10.1371/journal.ppat.1006918] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
The malaria-causing blood stage of Plasmodium falciparum requires extracellular pantothenate for proliferation. The parasite converts pantothenate into coenzyme A (CoA) via five enzymes, the first being a pantothenate kinase (PfPanK). Multiple antiplasmodial pantothenate analogues, including pantothenol and CJ-15,801, kill the parasite by targeting CoA biosynthesis/utilisation. Their mechanism of action, however, remains unknown. Here, we show that parasites pressured with pantothenol or CJ-15,801 become resistant to these analogues. Whole-genome sequencing revealed mutations in one of two putative PanK genes (Pfpank1) in each resistant line. These mutations significantly alter PfPanK activity, with two conferring a fitness cost, consistent with Pfpank1 coding for a functional PanK that is essential for normal growth. The mutants exhibit a different sensitivity profile to recently-described, potent, antiplasmodial pantothenate analogues, with one line being hypersensitive. We provide evidence consistent with different pantothenate analogue classes having different mechanisms of action: some inhibit CoA biosynthesis while others inhibit CoA-utilising enzymes. The coenzyme A (CoA) biosynthetic pathway is under investigation as a target for the development of drugs aimed at several infectious agents, including malaria parasites. To synthesise CoA, the parasite scavenges the essential precursor pantothenate (vitamin B5). Several pantothenate analogues possess potent (nM) activity against the parasite, but their exact mechanism of action is unknown. We have generated mutant parasites that are resistant or hypersensitive to various pantothenate analogues. These parasites harbour mutations in a gene we now show codes for the first enzyme in the CoA biosynthesis pathway. This enzyme is not the target of the analogues, but instead converts them into antimetabolites that, depending on the analogue, either inhibit a CoA biosynthesis enzyme or downstream CoA-utilising enzymes.
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Affiliation(s)
- Erick T. Tjhin
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Alan L. Sewell
- Department of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Annabelle Hoegl
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Leanne Barnard
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Anna E. Sexton
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Ghizal Siddiqui
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Vanessa M. Howieson
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Alexander G. Maier
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Darren J. Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Rodolfo Marquez
- Department of Chemistry, University of Glasgow, Glasgow, United Kingdom
- Department of Chemistry, Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Kevin J. Saliba
- Research School of Biology, The Australian National University, Canberra, Australia
- Medical School, The Australian National University, Canberra, Australia
- * E-mail:
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20
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Arnott ZLP, Nozaki S, Monteiro DCF, Morgan HE, Pearson AR, Niki H, Webb ME. The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ·AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Biochemistry 2017; 56:4931-4939. [PMID: 28832133 PMCID: PMC5724930 DOI: 10.1021/acs.biochem.7b00509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
antimetabolite pentyl pantothenamide has broad spectrum antibiotic
activity but exhibits enhanced activity against Escherichia
coli. The PanDZ complex has been proposed to regulate the
pantothenate biosynthetic pathway in E. coli by limiting
the supply of β-alanine in response to coenzyme A concentration.
We show that formation of such a complex between activated aspartate
decarboxylase (PanD) and PanZ leads to sequestration of the pyruvoyl
cofactor as a ketone hydrate and demonstrate that both PanZ overexpression-linked
β-alanine auxotrophy and pentyl pantothenamide toxicity are
due to formation of this complex. This both demonstrates that the
PanDZ complex regulates pantothenate biosynthesis in a cellular context
and validates the complex as a target for antibiotic development.
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Affiliation(s)
- Zoe L P Arnott
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K.,Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Shingo Nozaki
- Microbial Genetics Laboratory, Genetics Strains Research Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Diana C F Monteiro
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K.,Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Holly E Morgan
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K
| | - Arwen R Pearson
- Hamburg Center for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, University of Hamburg , Luruper Chaussee 149, Hamburg 22761, Germany
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetics Strains Research Center, National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, Graduate University for Advanced Studies (Sokendai) , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds , Leeds LS2 9JT, U.K
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21
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Ogata Y, Chohnan S. Prokaryotic type III pantothenate kinase enhances coenzyme A biosynthesis in Escherichia coli. J GEN APPL MICROBIOL 2016; 61:266-9. [PMID: 26782658 DOI: 10.2323/jgam.61.266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuta Ogata
- Department of Applied Life Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
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22
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Hughes SJ, Barnard L, Mottaghi K, Tempel W, Antoshchenko T, Hong BS, Allali-Hassani A, Smil D, Vedadi M, Strauss E, Park HW. Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product. ACS Infect Dis 2016; 2:627-641. [PMID: 27759386 DOI: 10.1021/acsinfecdis.6b00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanKII), the first enzyme of coenzyme A biosynthesis. This mechanism of action follows from SaPanKII having a binding mode for PanAms that is distinct from those of other PanKs. To dissect the molecular interactions responsible for PanAm inhibitory activity, we conducted a mini SAR study in tandem with the cocrystallization of SaPanKII with two classic PanAms (N5-Pan and N7-Pan), culminating in the synthesis and characterization of two new PanAms, N-Pip-PanAm and MeO-N5-PanAm. The cocrystal structures showed that all of the PanAms are phosphorylated by SaPanKII but remain bound at the active site; this occurs primarily through interactions with Tyr240' and Thr172'. Kinetic analysis showed a strong correlation between kcat (slow PanAm turnover) and IC50 (inhibition of pantothenate phosphorylation) values, suggesting that SaPanKII inhibition occurs via a delay in product release. In-depth analysis of the PanAm-bound structures showed that the capacity for accepting a hydrogen bond from the amide of Thr172' was a stronger determinant for PanAm potency than the capacity to π-stack with Tyr240'. The two new PanAms, N-Pip-PanAm and MeO-N5-PanAm, effectively combine both hydrogen bonding and hydrophobic interactions, resulting in the most potent SaPanKII inhibition described to date. Taken together, our results are consistent with an inhibition mechanism wherein PanAms act as SaPanKII substrates that remain bound upon phosphorylation. The phospho-PanAm-SaPanKII interactions described herein may help future antistaphylococcal drug development.
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Affiliation(s)
| | - Leanne Barnard
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | | | | | - Tetyana Antoshchenko
- Department
of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112, United States
| | | | | | | | | | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hee-Won Park
- Department
of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112, United States
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23
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Subramanian C, Yun MK, Yao J, Sharma LK, Lee RE, White SW, Jackowski S, Rock CO. Allosteric Regulation of Mammalian Pantothenate Kinase. J Biol Chem 2016; 291:22302-22314. [PMID: 27555321 DOI: 10.1074/jbc.m116.748061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 12/21/2022] Open
Abstract
Pantothenate kinase is the master regulator of CoA biosynthesis and is feedback-inhibited by acetyl-CoA. Comparison of the human PANK3·acetyl-CoA complex to the structures of PANK3 in four catalytically relevant complexes, 5'-adenylyl-β,γ-imidodiphosphate (AMPPNP)·Mg2+, AMPPNP·Mg2+·pantothenate, ADP·Mg2+·phosphopantothenate, and AMP phosphoramidate (AMPPN)·Mg2+, revealed a large conformational change in the dimeric enzyme. The amino-terminal nucleotide binding domain rotates to close the active site, and this allows the P-loop to engage ATP and facilitates required substrate/product interactions at the active site. Biochemical analyses showed that the transition between the inactive and active conformations, as assessed by the binding of either ATP·Mg2+ or acyl-CoA to PANK3, is highly cooperative indicating that both protomers move in concert. PANK3(G19V) cannot bind ATP, and biochemical analyses of an engineered PANK3/PANK3(G19V) heterodimer confirmed that the two active sites are functionally coupled. The communication between the two protomers is mediated by an α-helix that interacts with the ATP-binding site at its amino terminus and with the substrate/inhibitor-binding site of the opposite protomer at its carboxyl terminus. The two α-helices within the dimer together with the bound ligands create a ring that stabilizes the assembly in either the active closed conformation or the inactive open conformation. Thus, both active sites of the dimeric mammalian pantothenate kinases coordinately switch between the on and off states in response to intracellular concentrations of ATP and its key negative regulators, acetyl(acyl)-CoA.
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Affiliation(s)
| | | | | | - Lalit Kumar Sharma
- Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Richard E Lee
- Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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24
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Abstract
Pantothenate is vitamin B5 and is the key precursor for the biosynthesis of coenzyme A (CoA), a universal and essential cofactor involved in a myriad of metabolic reactions, including the synthesis of phospholipids, the synthesis and degradation of fatty acids, and the operation of the tricarboxylic acid cycle. CoA is also the only source of the phosphopantetheine prosthetic group for enzymes that shuttle intermediates between the active sites of enzymes involved in fatty acid, nonribosomal peptide, and polyketide synthesis. Pantothenate can be synthesized de novo and/or transported into the cell through a pantothenatepermease. Pantothenate uptake is essential for those organisms that lack the genes to synthesize this vitamin. The intracellular levels of CoA are controlled by the balance between synthesis and degradation. In particular, CoA is assembled in five enzymatic steps, starting from the phosphorylation of pantothenate to phosphopantothenatecatalyzed by pantothenate kinase, the product of the coaA gene. In some bacteria, the production of phosphopantothenate by pantothenate kinase is the rate limiting and most regulated step in the biosynthetic pathway. CoA synthesis additionally networks with other vitamin-associated pathways, such as thiamine and folic acid.
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25
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Recent advances in targeting coenzyme A biosynthesis and utilization for antimicrobial drug development. Biochem Soc Trans 2015; 42:1080-6. [PMID: 25110006 DOI: 10.1042/bst20140131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The biosynthesis and utilization of CoA (coenzyme A), the ubiquitous and essential acyl carrier in all organisms, have long been regarded as excellent targets for the development of new antimicrobial drugs. Moreover, bioinformatics and biochemical studies have highlighted significant differences between several of the bacterial enzyme targets and their human counterparts, indicating that selective inhibition of the former should be possible. Over the past decade, a large amount of structural and mechanistic data has been gathered on CoA metabolism and the CoA biosynthetic enzymes, and this has facilitated the discovery and development of several promising candidate antimicrobial agents. These compounds include both target-specific inhibitors, as well as CoA antimetabolite precursors that can reduce CoA levels and interfere with processes that are dependent on this cofactor. In the present mini-review we provide an overview of the most recent of these studies that, taken together, have also provided chemical validation of CoA biosynthesis and utilization as viable targets for antimicrobial drug development.
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26
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de Villiers M, Barnard L, Koekemoer L, Snoep JL, Strauss E. Variation in pantothenate kinase type determines the pantothenamide mode of action and impacts on coenzyme A salvage biosynthesis. FEBS J 2014; 281:4731-53. [PMID: 25156889 DOI: 10.1111/febs.13013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/18/2014] [Accepted: 08/18/2014] [Indexed: 11/28/2022]
Abstract
N-substituted pantothenamides are analogues of pantothenic acid, the vitamin precursor of CoA, and constitute a class of well-studied bacterial growth inhibitors that show potential as new antibacterial agents. Previous studies have highlighted the importance of pantothenate kinase (PanK; EC 2.7.1.33) (the first enzyme of CoA biosynthesis) in mediating pantothenamide-induced growth inhibition by one of two proposed mechanisms: first, by acting on the pantothenamides as alternate substrates (allowing their conversion into CoA antimetabolites, with subsequent effects on CoA- and acyl carrier protein-dependent processes) or, second, by being directly inhibited by them (causing a reduction in CoA biosynthesis). In the present study we used structurally modified pantothenamides to probe whether PanKs interact with these compounds in the same manner. We show that the three distinct types of eubacterial PanKs that are known to exist (PanKI , PanKII and PanKIII ) respond very differently and, consequently, are responsible for determining the pantothenamide mode of action in each case: although the promiscuous PanKI enzymes accept them as substrates, the highly selective PanKIII s are resistant to their inhibitory effects. Most unexpectedly, Staphylococcus aureus PanK (the only known example of a bacterial PanKII ) experiences uncompetitive inhibition in a manner that is described for the first time. In addition, we show that pantetheine, a CoA degradation product that closely resembles the pantothenamides, causes the same effect. This suggests that, in S. aureus, pantothenamides may act by usurping a previously unknown role of pantetheine in the regulation of CoA biosynthesis, and validates its PanK as a target for the development of new antistaphylococcal agents.
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27
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Chohnan S, Murase M, Kurikawa K, Higashi K, Ogata Y. Antimicrobial activity of pantothenol against staphylococci possessing a prokaryotic type II pantothenate kinase. Microbes Environ 2014; 29:224-6. [PMID: 24759689 PMCID: PMC4103530 DOI: 10.1264/jsme2.me13178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/01/2014] [Indexed: 11/12/2022] Open
Abstract
Pantothenol is a provitamin of pantothenic acid (vitamin B5) that is widely used in healthcare and cosmetic products. This analog of pantothenate has been shown to markedly inhibit the phosphorylation activity of the prokaryotic type II pantothenate kinase of Staphylococcus aureus, which catalyzes the first step of the coenzyme A biosynthetic pathway. Since type II enzymes are found exclusively in staphylococci, pantothenol suppresses the growth of S. aureus, S. epidermidis, and S. saprophyticus, which inhabit the skin of humans. Therefore, the addition of this provitamin to ointment and skincare products may be highly effective in preventing infections by opportunistic pathogens.
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Affiliation(s)
- Shigeru Chohnan
- Department of Bioresource Science, Ibaraki University College of Agriculture, 3–21–1 Chuo, Ami, Ibaraki 300–0393, Japan
- Department of Applied Life Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3–5–8 Saiwai, Fuchu, Tokyo 183–8509, Japan
| | - Misa Murase
- Department of Bioresource Science, Ibaraki University College of Agriculture, 3–21–1 Chuo, Ami, Ibaraki 300–0393, Japan
| | - Kota Kurikawa
- Department of Bioresource Science, Ibaraki University College of Agriculture, 3–21–1 Chuo, Ami, Ibaraki 300–0393, Japan
| | - Kodai Higashi
- Department of Bioresource Science, Ibaraki University College of Agriculture, 3–21–1 Chuo, Ami, Ibaraki 300–0393, Japan
| | - Yuta Ogata
- Department of Applied Life Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3–5–8 Saiwai, Fuchu, Tokyo 183–8509, Japan
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Ogata Y, Katoh H, Asayama M, Chohnan S. Role of prokaryotic type I and III pantothenate kinases in the coenzyme A biosynthetic pathway of Bacillus subtilis. Can J Microbiol 2014; 60:297-305. [PMID: 24784177 DOI: 10.1139/cjm-2013-0793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pantothenate kinases (CoaAs) catalyze the phosphorylation of pantothenate in the first step of the coenzyme A (CoA) biosynthetic pathway. These bacterial enzymes have been categorized into 3 types, the prokaryotic type I, II, and III CoaAs. Bacteria typically carry a single CoaA gene on their genome, but Bacillus subtilis possesses 2 proteins homologous to type I and III CoaAs, known as BsCoaA and BsCoaX, respectively. Both recombinant proteins exhibited the expected kinase activity and the characteristic properties of type I and III CoaAs, i.e., regulation by CoASH and acyl-CoAs in BsCoaA and the requirement of a monovalent cation in BsCoaX. Both gene disruptants appeared to grow in a manner similar to the wild-type strain. With the BsCoaX disruptant, the BsCoaA had the ability to completely fill the intracellular CoA pool, whereas the BsCoaA disruptant did not. These findings clearly indicate that these 2 CoaAs are employed together in the CoA biosynthetic pathway in B. subtilis and that the contribution of the type I CoaA (BsCoaA) to the formation of the intracellular CoA pool is larger than that of the type III CoaA (BsCoaX).
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Affiliation(s)
- Yuta Ogata
- Department of Bioresource Science, Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami, Ibaraki 300-0393, Japan
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Schacherl M, Waltersperger S, Baumann U. Structural characterization of the ribonuclease H-like type ASKHA superfamily kinase MK0840 from Methanopyrus kandleri. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2440-50. [PMID: 24311585 DOI: 10.1107/s0907444913022683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022]
Abstract
Murein recycling is a process in which microorganisms recover peptidoglycan-degradation products in order to utilize them in cell wall biosynthesis or basic metabolic pathways. Methanogens such as Methanopyrus kandleri contain pseudomurein, which differs from bacterial murein in its composition and branching. Here, four crystal structures of the putative sugar kinase MK0840 from M. kandleri in apo and nucleotide-bound states are reported. MK0840 shows high similarity to bacterial anhydro-N-acetylmuramic acid kinase, which is involved in murein recycling. The structure shares a common fold with panthothenate kinase and the 2-hydroxyglutaryl-CoA dehydratase component A, both of which are members of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases. Local conformational changes in the nucleotide-binding site between the apo and holo forms are observed upon nucleotide binding. Further insight is given into domain movements and putative active-site residues are identified.
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Affiliation(s)
- Magdalena Schacherl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, 50674 Cologne, Germany
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30
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Combination of pantothenamides with vanin inhibitors as a novel antibiotic strategy against gram-positive bacteria. Antimicrob Agents Chemother 2013; 57:4794-800. [PMID: 23877685 DOI: 10.1128/aac.00603-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The emergence of resistance against current antibiotics calls for the development of new compounds to treat infectious diseases. Synthetic pantothenamides are pantothenate analogs that possess broad-spectrum antibacterial activity in vitro in minimal media. Pantothenamides were shown to be substrates of the bacterial coenzyme A (CoA) biosynthetic pathway, causing cellular CoA depletion and interference with fatty acid synthesis. In spite of their potential use and selectivity for bacterial metabolic routes, these compounds have never made it to the clinic. In the present study, we show that pantothenamides are not active as antibiotics in the presence of serum, and we found that they were hydrolyzed by ubiquitous pantetheinases of the vanin family. To address this further, we synthesized a series of pantetheinase inhibitors based on a pantothenate scaffold that inhibited serum pantetheinase activity in the nanomolar range. Mass spectrometric analysis showed that addition of these pantetheinase inhibitors prevented hydrolysis of pantothenamides by serum. We found that combinations of these novel pantetheinase inhibitors and prototypic pantothenamides like N5-Pan and N7-Pan exerted antimicrobial activity in vitro, particularly against Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, and Streptococcus pyogenes) even in the presence of serum. These results indicate that pantothenamides, when protected against degradation by host pantetheinases, are potentially useful antimicrobial agents.
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Katoh H, Tamaki H, Tokutake Y, Hanada S, Chohnan S. Identification of pantoate kinase and phosphopantothenate synthetase from Methanospirillum hungatei. J Biosci Bioeng 2012. [PMID: 23200110 DOI: 10.1016/j.jbiosc.2012.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pantothenate synthetase (PanC) and pantothenate kinase which function in the canonical coenzyme A (CoA) biosynthetic pathway cannot be found in most archaea. COG1829 and COG1701 intrinsic to archaea were proposed as the candidate proteins for producing 4'-phosphopantothenate instead, and the COG1701 protein from Methanosarcina mazei was assigned as PanC. Meanwhile, the Thermococcus kodakarensis COG1829 and COG1701 proteins were biochemically identified as novel enzymes, i.e., pantoate kinase (PoK) and phosphopantothenate synthetase (PPS). In this study, the functions of Mhun_0831 (COG1829) and Mhun_0832 (COG1701) from Methanospirillum hungatei were identified, and the recombinant enzymes were partially characterized. Plasmids simultaneously possessing the two genes encoding Mhun_0831 and Mhun_0832 complemented the poor growth of the temperature-sensitive Escherichia coli pantothenate kinase mutant ts9. The recombinant Mhun_0831 and Mhun_0832 expressed in E. coli cells exhibited PoK and PPS activities, respectively, being in accord with the functions of T. kodakarensis proteins. The PoK activity was most active at pH 8.5 and 40°C, and accepted ATP and UTP as a phosphate donor. Although CoA did not affect the PoK activity, the end product considerably accelerated the PPS activity. The homologs of both proteins are widely conserved in most archaeal genomes. Taken together, our findings indicate that archaea can synthesize CoA through the unique pathway involving PoK and PPS, in addition to the canonical one that the order Thermoplasmatales employs.
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Affiliation(s)
- Hiroki Katoh
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ibaraki, Japan
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van der Westhuyzen R, Hammons JC, Meier JL, Dahesh S, Moolman WJA, Pelly SC, Nizet V, Burkart MD, Strauss E. The antibiotic CJ-15,801 is an antimetabolite that hijacks and then inhibits CoA biosynthesis. ACTA ACUST UNITED AC 2012; 19:559-71. [PMID: 22633408 DOI: 10.1016/j.chembiol.2012.03.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/13/2012] [Accepted: 03/27/2012] [Indexed: 01/21/2023]
Abstract
The natural product CJ-15,801 is an inhibitor of Staphylococcus aureus, but not other bacteria. Its close structural resemblance to pantothenic acid, the vitamin precursor of coenzyme A (CoA), and its Michael acceptor moiety suggest that it irreversibly inhibits an enzyme involved in CoA biosynthesis or utilization. However, its mode of action and the basis for its specificity have not been elucidated to date. We demonstrate that CJ-15,801 is transformed by the uniquely selective S. aureus pantothenate kinase, the first CoA biosynthetic enzyme, into a substrate for the next enzyme, phosphopantothenoylcysteine synthetase, which is inhibited through formation of a tight-binding structural mimic of its native reaction intermediate. These findings reveal CJ-15,801 as a vitamin biosynthetic pathway antimetabolite with a mechanism similar to that of the sulfonamide antibiotics and highlight CoA biosynthesis as a viable antimicrobial drug target.
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Williams PM, Sheldrake GN, Macdonald SJ, Hamilton CJ. A chemoenzymatic synthesis of 5a-carba-α-d-mannose-6-phosphate. Carbohydr Res 2011; 346:1257-61. [DOI: 10.1016/j.carres.2011.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/02/2011] [Accepted: 04/06/2011] [Indexed: 11/29/2022]
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35
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Leonardi R, Zhang YM, Yun MK, Zhou R, Zeng FY, Lin W, Cui J, Chen T, Rock CO, White SW, Jackowski S. Modulation of pantothenate kinase 3 activity by small molecules that interact with the substrate/allosteric regulatory domain. ACTA ACUST UNITED AC 2011; 17:892-902. [PMID: 20797618 DOI: 10.1016/j.chembiol.2010.06.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/04/2010] [Accepted: 06/07/2010] [Indexed: 11/30/2022]
Abstract
Pantothenate kinase (PanK) catalyzes the rate-controlling step in coenzyme A (CoA) biosynthesis. PanK3 is stringently regulated by acetyl-CoA and uses an ordered kinetic mechanism with ATP as the leading substrate. Biochemical analysis of site-directed mutants indicates that pantothenate binds in a tunnel adjacent to the active site that is occupied by the pantothenate moiety of the acetyl-CoA regulator in the PanK3acetyl-CoA binary complex. A high-throughput screen for PanK3 inhibitors and activators was applied to a bioactive compound library. Thiazolidinediones, sulfonylureas and steroids were inhibitors, and fatty acyl-amides and tamoxifen were activators. The PanK3 activators and inhibitors either stimulated or repressed CoA biosynthesis in HepG2/C3A cells. The flexible allosteric acetyl-CoA regulatory domain of PanK3 also binds the substrates, pantothenate and pantetheine, and small molecule inhibitors and activators to modulate PanK3 activity.
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Affiliation(s)
- Roberta Leonardi
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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36
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Rootman I, de Villiers M, Brand LA, Strauss E. Creating Cellulose-Binding Domain Fusions of the Coenzyme A Biosynthetic Enzymes to Enable Reactor-Based Biotransformations. ChemCatChem 2010. [DOI: 10.1002/cctc.201000197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Pantothenate kinase from the thermoacidophilic archaeon Picrophilus torridus. J Bacteriol 2010; 192:233-41. [PMID: 19854913 DOI: 10.1128/jb.01021-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pantothenate kinase (CoaA) catalyzes the first step of the coenzyme A (CoA) biosynthetic pathway and controls the intracellular concentrations of CoA through feedback inhibition in bacteria. An alternative enzyme found in archaea, pantoate kinase, is missing in the order Thermoplasmatales. The PTO0232 gene from Picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type I CoaA. The cloned gene clearly complements the poor growth of the temperature-sensitive Escherichia coli CoaA mutant strain ts9, and the recombinant protein expressed in E. coli cells transfers phosphate to pantothenate at pH 5 and 55 degrees C. In contrast to E. coli CoaA, the P. torridus enzyme is refractory to feedback regulation by CoA, indicating that in P. torridus cells the CoA levels are not regulated by the CoaA step. These data suggest the existence of two subtypes within the class of prokaryotic type I CoaAs.
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Rowan AS, Nicely NI, Cochrane N, Wlassoff WA, Claiborne A, Hamilton CJ. Nucleoside triphosphate mimicry: a sugar triazolyl nucleoside as an ATP-competitive inhibitor of B. anthracis pantothenate kinase. Org Biomol Chem 2009; 7:4029-36. [PMID: 19763307 PMCID: PMC6074028 DOI: 10.1039/b909729e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of a library of nucleoside triphosphate mimetics is described where the Mg(2+) chelated triphosphate sidechain is replaced by an uncharged methylene-triazole linked monosaccharide sidechain. The compounds have been evaluated as inhibitors of Bacillus anthracis pantothenate kinase and a competitive inhibitor has been identified with a K(i) that is 3-fold lower than the K(m) value of ATP.
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Affiliation(s)
- Andrew S Rowan
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG
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40
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Retraction: Open and closed conformations reveal induced fit movements in butyrate kinase 2 activation. J. Diao, Y. D. Ma, and M. S. Hasson. Proteins 2009; 80:1712. [DOI: 10.1002/prot.22610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/22/2009] [Accepted: 08/26/2009] [Indexed: 11/08/2022]
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41
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Wu Z, Li C, Lv S, Zhou B. Pantothenate kinase-associated neurodegeneration: insights from a Drosophila model. Hum Mol Genet 2009; 18:3659-72. [PMID: 19602483 DOI: 10.1093/hmg/ddp314] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pantothenate-Kinase-Associated-Neurodegeneration (PKAN) is a devastating disease, resulting from mutations in pantothenate kinase 2 (PANK2), one of the four human pantothenate kinase genes (PANK1-4). Interestingly, PanK2 appears to be the only mitochondria-targeted human PanK. It is unknown whether the mitochondria-targeted PanK is associated with any unique function, nor whether PKAN is due solely to the loss of pantothenate kinase activity. Drosophila PANK [fumble (fbl)] encodes several isoforms of pantothenate kinase products, one of which localizes to mitochondria and the others cytosol. fbl flies exhibit many characteristic features reminiscent of PKAN patients. Various forms of Drosophila fbl and human PANK2 were introduced into fbl flies to study their in vivo functions. Only mitochondria-targeted Fbl or human PanK2 was able to rescue fbl mutation, with the rescuing ability sensitive to the expression level of the transgene. Transgenic lines with low expression of normal Fbl or PanK2 displayed similar phenotypes as PANK2 mutant transgenic flies. These PanK2 mutants all showed reduced and phenotype severity-correlated in vitro pantothenate kinase activities. Amazingly, cytosolic PanK3 and PanK4 could mostly, but not fully, rescue fbl defects except the male sterility. Therefore, fbl appears to be the orthologue of human PANK2, and PanK2 is functionally more potent than PanK3 and PanK4 in vivo. We suggest that mitochondria-located pantothenate kinase is required to achieve the maximal enzymatic activity to fulfill the most challenging task such as maintaining male fertility and optimal neuronal functions, and PKAN features are mainly due to the reduction of the total cellular pantothenate kinase activity in the most susceptible regions.
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Affiliation(s)
- Zhihao Wu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
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The type III pantothenate kinase encoded by coaX is essential for growth of Bacillus anthracis. J Bacteriol 2008; 190:6271-5. [PMID: 18641144 DOI: 10.1128/jb.00860-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In Bacillus anthracis, the novel type III pantothenate kinase (PanK(Ba); encoded by coaX) catalyzes the first committed step in coenzyme A biosynthesis. We have demonstrated by analyzing the growth characteristics of a conditional coaX mutant that PanK(Ba) is an essential enzyme, thus contributing to its validation as a new antimicrobial target.
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Abstract
Pantothenic acid, a precursor of coenzyme A (CoA), is essential for the growth of pathogenic microorganisms. Since the structure of pantothenic acid was determined, many analogues of this essential metabolite have been prepared. Several have been demonstrated to exert an antimicrobial effect against a range of microorganisms by inhibiting the utilization of pantothenic acid, validating pantothenic acid utilization as a potential novel antimicrobial drug target. This review commences with an overview of the mechanisms by which various microorganisms acquire the pantothenic acid they require for growth, and the universal CoA biosynthesis pathway by which pantothenic acid is converted into CoA. A detailed survey of studies that have investigated the inhibitory activity of analogues of pantothenic acid and other precursors of CoA follows. The potential of inhibitors of both pantothenic acid utilization and biosynthesis as novel antibacterial, antifungal and antimalarial agents is discussed, focusing on inhibitors and substrates of pantothenate kinase, the enzyme catalysing the rate-limiting step of CoA biosynthesis in many organisms. The best strategies are considered for identifying inhibitors of pantothenic acid utilization and biosynthesis that are potent and selective inhibitors of microbial growth and that may be suitable for use as chemotherapeutic agents in humans.
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Affiliation(s)
- Christina Spry
- School of Biochemistry and Molecular Biology, The Australian National University, Canberra, Australia
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44
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Hong BS, Senisterra G, Rabeh WM, Vedadi M, Leonardi R, Zhang YM, Rock CO, Jackowski S, Park HW. Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder. J Biol Chem 2007; 282:27984-93. [PMID: 17631502 DOI: 10.1074/jbc.m701915200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pantothenate kinase (PanK) catalyzes the first step in CoA biosynthesis and there are three human genes that express four isoforms with highly conserved catalytic core domains. Here we report the homodimeric structures of the catalytic cores of PanK1alpha and PanK3 in complex with acetyl-CoA, a feedback inhibitor. Each monomer adopts a fold of the actin kinase superfamily and the inhibitor-bound structures explain the basis for the allosteric regulation by CoA thioesters. These structures also provide an opportunity to investigate the structural effects of the PanK2 mutations that have been implicated in neurodegeneration. Biochemical and thermodynamic analyses of the PanK3 mutant proteins corresponding to PanK2 mutations show that mutant proteins with compromised activities and/or stabilities correlate with a higher incidence of the early onset of disease.
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Affiliation(s)
- Bum Soo Hong
- Structural Genomics Consortium and Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
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45
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Nicely NI, Parsonage D, Paige C, Newton GL, Fahey RC, Leonardi R, Jackowski S, Mallett TC, Claiborne A. Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology. Biochemistry 2007; 46:3234-45. [PMID: 17323930 PMCID: PMC2613803 DOI: 10.1021/bi062299p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coenzyme A (CoASH) is the major low-molecular weight thiol in Staphylococcus aureus and a number of other bacteria; the crystal structure of the S. aureus coenzyme A-disulfide reductase (CoADR), which maintains the reduced intracellular state of CoASH, has recently been reported [Mallett, T.C., Wallen, J.R., Karplus, P.A., Sakai, H., Tsukihara, T., and Claiborne, A. (2006) Biochemistry 45, 11278-89]. In this report we demonstrate that CoASH is the major thiol in Bacillus anthracis; a bioinformatics analysis indicates that three of the four proteins responsible for the conversion of pantothenate (Pan) to CoASH in Escherichia coli are conserved in B. anthracis. In contrast, a novel type III pantothenate kinase (PanK) catalyzes the first committed step in the biosynthetic pathway in B. anthracis; unlike the E. coli type I PanK, this enzyme is not subject to feedback inhibition by CoASH. The crystal structure of B. anthracis PanK (BaPanK), solved using multiwavelength anomalous dispersion data and refined at a resolution of 2.0 A, demonstrates that BaPanK is a new member of the Acetate and Sugar Kinase/Hsc70/Actin (ASKHA) superfamily. The Pan and ATP substrates have been modeled into the active-site cleft; in addition to providing a clear rationale for the absence of CoASH inhibition, analysis of the Pan-binding pocket has led to the development of two new structure-based motifs (the PAN and INTERFACE motifs). Our analyses also suggest that the type III PanK in the spore-forming B. anthracis plays an essential role in the novel thiol/disulfide redox biology of this category A biodefense pathogen.
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Affiliation(s)
- Nathan I Nicely
- Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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46
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Leonardi R, Rock CO, Jackowski S, Zhang YM. Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine. Proc Natl Acad Sci U S A 2007; 104:1494-9. [PMID: 17242360 PMCID: PMC1785270 DOI: 10.1073/pnas.0607621104] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human isoform 2 of pantothenate kinase (PanK2) is localized to the mitochondria, and mutations in this protein are associated with a progressive neurodegenerative disorder. PanK2 inhibition by acetyl-CoA is so stringent (IC50 < 1 microM) that it is unclear how the enzyme functions in the presence of intracellular CoA concentrations. Palmitoylcarnitine was discovered to be a potent activator of PanK2 that functions to competitively antagonize acetyl-CoA inhibition. Acetyl-CoA was a competitive inhibitor of purified PanK2 with respect to ATP. The interaction between PanK2 and acetyl-CoA was stable enough that a significant proportion of the purified protein was isolated as the PanK2.acetyl-CoA complex. The long-chain acylcarnitine activation of PanK2 explains how PanK2 functions in vivo, by providing a positive regulatory mechanism to counteract the negative regulation of PanK2 activity by acetyl-CoA. Our results suggest that PanK2 is located in the mitochondria to sense the levels of palmitoylcarnitine and up-regulate CoA biosynthesis in response to an increased mitochondrial demand for the cofactor to support beta-oxidation.
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Affiliation(s)
- Roberta Leonardi
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Charles O. Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Yong-Mei Zhang
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
- *To whom correspondence should be addressed. E-mail:
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