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Li S, Lao J, Sun Y, Hua X, Lin P, Wang F, Shen G, Zhao P, Xia Q. CRISPR/Cas9-Mediated Editing of BmEcKL1 Gene Sequence Affected Silk Gland Development of Silkworms ( Bombyx mori). Int J Mol Sci 2024; 25:1907. [PMID: 38339188 PMCID: PMC10856159 DOI: 10.3390/ijms25031907] [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: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The silkworm (Bombyx mori) has served humankind through silk protein production. However, traditional sericulture and the silk industry have encountered considerable bottlenecks and must rely on major technological breakthroughs to keep up with the current rapid developments. The adoption of gene editing technology has nevertheless brought new hope to traditional sericulture and the silk industry. The long period and low efficiency of traditional genetic breeding methods to obtain high silk-yielding silkworm strains have hindered the development of the sericulture industry; the use of gene editing technology to specifically control the expression of genes related to silk gland development or silk protein synthesis is beneficial for obtaining silkworm strains with excellent traits. In this study, BmEcKL1 was specifically knocked out in the middle (MSGs) and posterior (PSGs) silk glands using CRISPR/Cas9 technology, and ΔBmEcKL1-MSG and ΔBmEcKL1-PSG strains with improved MSGs and PSGs and increased silk production were obtained. This work identifies and proves that BmEcKL1 directly or indirectly participates in silk gland development and silk protein synthesis, providing new perspectives for investigating silk gland development and silk protein synthesis mechanisms in silkworms, which is of great significance for selecting and breeding high silk-yielding silkworm varieties.
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Affiliation(s)
- Shimin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
| | - Junjie Lao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
| | - Yue Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
| | - Xiaoting Hua
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ping Lin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Feng Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Guanwang Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400716, China; (S.L.); (J.L.); (X.H.); (P.L.); (F.W.); (G.S.); (P.Z.)
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China
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2
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Biological Evaluation of New Thienopyridinium and Thienopyrimidinium Derivatives as Human Choline Kinase Inhibitors. Pharmaceutics 2022; 14:pharmaceutics14040715. [PMID: 35456549 PMCID: PMC9032693 DOI: 10.3390/pharmaceutics14040715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 12/10/2022] Open
Abstract
Due to its role in lipid biosynthesis, choline kinase α1 (CKα1) is an interesting target for the development of new antitumor agents. In this work, we present a series of 41 compounds designed based on the well-known and successful strategy of introducing thienopyridine and pyrimidine as bioisosteres of other heterocycles in active antitumor compounds. Notwithstanding the fact that some of these compounds do not show significant enzymatic inhibition, others, in contrast, feature substantially improved enzymatic and antiproliferative inhibition values. This is also confirmed by docking analysis, whereby compounds with longer linkers and thienopyrimidine cationic head have been identified as the most compelling. Among the best compounds is Ff-35, which inhibits the growth of different tumor cells at submicromolar concentrations. Moreover, Ff-35 is more potent in inhibiting CKα1 than other previous biscationic derivatives. Treatment of A549, Hela, and MDA-MB-231 cells with Ff-35 results in their arrest at the G1 phase of the cell cycle. Furthermore, the compound induces cellular apoptosis in a concentration-dependent manner. Altogether, these findings indicate that Ff-35 is a promising new chemotherapeutic agent with encouraging preclinical potential.
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Li TT, Yang J, Huo YY, Zeng ZY, Huang HY, Xu FR, Dong X. Control of pathogenic fungi on Panax notoginseng by volatile oils from the food ingredients Allium sativum and Foeniculum vulgare. Lett Appl Microbiol 2022; 75:89-102. [PMID: 35334116 DOI: 10.1111/lam.13706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
To screen natural drugs with strong inhibitory effects against pathogenic fungi related to P. notoginseng, the antifungal activities of garlic and fennel EOs were studied by targeting P. notoginseng disease-associated fungi, and the possible action mechanisms of garlic and fennel EOs as plant fungicides were preliminarily discussed. At present, the antifungal mechanism of EOs has not been fully established. Therefore, understanding the antifungal mechanism of plant EOs is helpful to address P. notoginseng diseases continuous cropping disease-related obstacles and other agricultural cultivation problems. First, the Oxford cup method and chessboard were used to confirm that the EOs and oxamyl had a significant inhibitory effect on the growth of Fusarium oxysporum. F. oxysporum is the main pathogen causing root rot of P. notoginseng and the preliminary study on the antifungal mechanisms of the EOs against F. oxysporum showed that the inhibition of EOs mainly affects cell membrane permeability, cell processes, and affects the enzyme activities of microorganism, to achieve antifungal effects. Finally an in vivo model verified that both two EOs could significantly inhibit the occurrence of root rot caused by F. oxysporum.
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Affiliation(s)
- Tian-Tian Li
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jing Yang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ying-Ying Huo
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Zi-Ying Zeng
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Heng-Yu Huang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Fu-Rong Xu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xian Dong
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
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4
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Quartieri F, Nesi M, Avanzi NR, Borghi D, Casale E, Corti E, Cucchi U, Donati D, Fasolini M, Felder ER, Galvani A, Giorgini ML, Lomolino A, Menichincheri M, Orrenius C, Perrera C, Re Depaolini S, Riccardi-Sirtori F, Salsi E, Isacchi A, Gnocchi P. Identification of unprecedented ATP-competitive choline kinase inhibitors. Bioorg Med Chem Lett 2021; 51:128310. [PMID: 34416377 DOI: 10.1016/j.bmcl.2021.128310] [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: 04/27/2021] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
In this article we describe the identification of unprecedented ATP-competitive ChoKα inhibitors starting from initial hit NMS-P830 that binds to ChoKα in an ATP concentration-dependent manner. This result is confirmed by the co-crystal structure of NMS-P830 in complex with Δ75-ChoKα. NMS-P830 is able to inhibit ChoKα in cells resulting in the reduction of intracellular phosphocholine formation. A structure-based medicinal chemistry program resulted in the identification of selective compounds that have good biochemical activity, solubility and metabolic stability and are suitable for further optimization. The ChoKα inhibitors disclosed in this article demonstrate for the first time the possibility to inhibit ChoKα with ATP-competitive compounds.
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Affiliation(s)
- Francesca Quartieri
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy.
| | - Marcella Nesi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Nilla R Avanzi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Daniela Borghi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Elena Casale
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Emiliana Corti
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Ulisse Cucchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Daniele Donati
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Marina Fasolini
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Eduard R Felder
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Arturo Galvani
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Maria L Giorgini
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Antonio Lomolino
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | | | - Christian Orrenius
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Claudia Perrera
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | | | | | - Enea Salsi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Antonella Isacchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Paola Gnocchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
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5
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Wang J, Zhang Y, Xu N, Zhang H, Fan Y, Rui C, Han M, Malik WA, Wang Q, Sun L, Chen X, Lu X, Wang D, Zhao L, Wang J, Wang S, Chen C, Guo L, Ye W. Genome-wide identification of CK gene family suggests functional expression pattern against Cd 2+ stress in Gossypium hirsutum L. Int J Biol Macromol 2021; 188:272-282. [PMID: 34364943 DOI: 10.1016/j.ijbiomac.2021.07.190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
Choline kinase (CK) gene plays an important role in plants growth, development and resistance to stress. It mainly regulates the biosynthesis of phosphatidylcholine. This study aims to explore the structure-function relationship, and to provide a framework for functional validation and biochemical characterization of various CK genes. Our analysis showed that 87 CK genes were identified in cotton and 7 diploid plants, of which 43 genes encode CK proteins in 4 cotton species, and 13 genes were identified in Gossypium hirsutum. Most of GhCK genes are affected by the abiotic stress conditions, indicating the importance of CK proteins for plant development and response to abiotic stress. RT-qPCR analysis showed the tissue specificity of GhCK genes in response to Cd2+ and other abiotic stresses. Under Cd2+ stress, the expression level of GhCK gene family members has undergone different changes. The expression level of GhCK5 was enhanced, indicating that Cd2+ stress caused the increase of phosphatidylcholine content, which in turn reacted on the plant cell membrane, finally reached the absorption of Cd2+ into plant cells to repair Cd2+ the purpose of contaminated soil. This study will further broaden our understanding of the association between evolution and function of the GhCK gene family.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Yuexin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Nan Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Hong Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Yapeng Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Cun Rui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Mingge Han
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Waqar Afzal Malik
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Qinqin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Liangqing Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Chao Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China.
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6
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Yang K, Rich JN. A delicate initiation: Lipolysis of lipid droplets fuels glioblastoma. Mol Cell 2021; 81:2686-2687. [PMID: 34214442 DOI: 10.1016/j.molcel.2021.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Liu et al. (2021) demonstrate that CHKα2 is capable of promoting lipolysis of lipid droplets through mechanisms that require sequential steps of post-translational modifications after glucose deprivation. Intriguingly, the oxidation of fatty acids derived from lipid droplets is essential for the survival of tumor cells that informs clinical outcome among glioblastoma patients.
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Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Jeremy N Rich
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania 15213, USA; Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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7
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Rubio-Ruiz B, Serrán-Aguilera L, Hurtado-Guerrero R, Conejo-García A. Recent advances in the design of choline kinase α inhibitors and the molecular basis of their inhibition. Med Res Rev 2020; 41:902-927. [PMID: 33103259 DOI: 10.1002/med.21746] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
Upregulated choline metabolism, characterized by an increase in phosphocholine (PCho), is a hallmark of oncogenesis and tumor progression. Choline kinase (ChoK), the enzyme responsible for PCho synthesis, has consequently become a promising drug target for cancer therapy and as such a significant number of ChoK inhibitors have been developed over the last few decades. More recently, due to the role of this enzyme in other pathologies, ChoK inhibitors have also been used in new therapeutic approaches against malaria and rheumatoid arthritis. Here, we review research results in the field of ChoKα inhibitors from their synthesis to the molecular basis of their binding mode. Strategies for the development of inhibitors and their selectivity on ChoKα over ChoKβ, the plasticity of the choline-binding site, the discovery of new exploitable binding sites, and the allosteric properties of this enzyme are highlighted. The outcomes summarized in this review will be a useful guide to develop new multifunctional potent drugs for the treatment of various human diseases.
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Affiliation(s)
- Belén Rubio-Ruiz
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain.,Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), SAS-University of Granada, Granada, Spain
| | - Lucía Serrán-Aguilera
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Ramón Hurtado-Guerrero
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.,Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.,Laboratorio de Microscopías Avanzada, University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
| | - Ana Conejo-García
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), SAS-University of Granada, Granada, Spain
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8
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Khalifa M, Few LL, See Too WC. ChoK-ing the Pathogenic Bacteria: Potential of Human Choline Kinase Inhibitors as Antimicrobial Agents. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1823485. [PMID: 32695809 PMCID: PMC7368946 DOI: 10.1155/2020/1823485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/25/2020] [Accepted: 06/29/2020] [Indexed: 01/12/2023]
Abstract
Novel antimicrobial agents are crucial to combat antibiotic resistance in pathogenic bacteria. Choline kinase (ChoK) in bacteria catalyzes the synthesis of phosphorylcholine, which is subsequently incorporated into the cell wall or outer membrane. In certain species of bacteria, phosphorylcholine is also used to synthesize membrane phosphatidylcholine. Numerous human ChoK inhibitors (ChoKIs) have been synthesized and tested for anticancer properties. Inhibition of S. pneumoniae ChoK by human ChoKIs showed a promising effect by distorting the cell wall and retarded the growth of this pathogen. Comparison of amino acid sequences at the catalytic sites of putative choline kinases from pathogenic bacteria and human enzymes revealed striking sequence conservation that supports the potential application of currently available ChoKIs for inhibiting bacterial enzymes. We also propose the combined use of ChoKIs and nanoparticles for targeted delivery to the pathogen while shielding the human host from any possible side effects of the inhibitors. More research should focus on the verification of putative bacterial ChoK activities and the characterization of ChoKIs with active enzymes. In conclusion, the presence of ChoK in a wide range of pathogenic bacteria and the distinct function of this enzyme has made it an attractive drug target. This review highlighted the possibility of "choking" bacterial ChoKs by using human ChoKIs.
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Affiliation(s)
- Moad Khalifa
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ling Ling Few
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Wei Cun See Too
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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9
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McMaster CR. From yeast to humans - roles of the Kennedy pathway for phosphatidylcholine synthesis. FEBS Lett 2017; 592:1256-1272. [PMID: 29178478 DOI: 10.1002/1873-3468.12919] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022]
Abstract
The major phospholipid present in most eukaryotic membranes is phosphatidylcholine (PC), comprising ~ 50% of phospholipid content. PC metabolic pathways are highly conserved from yeast to humans. The main pathway for the synthesis of PC is the Kennedy (CDP-choline) pathway. In this pathway, choline is converted to phosphocholine by choline kinase, phosphocholine is metabolized to CDP-choline by the rate-determining enzyme for this pathway, CTP:phosphocholine cytidylyltransferase, and cholinephosphotransferase condenses CDP-choline with diacylglycerol to produce PC. This Review discusses how PC synthesis via the Kennedy pathway is regulated, its role in cellular and biological processes, as well as diseases known to be associated with defects in PC synthesis. Finally, we present the first model for the making of a membrane via PC synthesis.
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10
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Pulido SA, Nguyen VH, Alzate JF, Cedeño DL, Makurath MA, Ríos-Vásquez A, Duque-Benítez SM, Jones MA, Robledo SM, Friesen JA. Insights into the phosphatidylcholine and phosphatidylethanolamine biosynthetic pathways in Leishmania parasites and characterization of a choline kinase from Leishmania infantum. Comp Biochem Physiol B Biochem Mol Biol 2017; 213:45-54. [PMID: 28754315 DOI: 10.1016/j.cbpb.2017.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/17/2017] [Accepted: 07/20/2017] [Indexed: 11/25/2022]
Abstract
The protozoan parasite Leishmania infantum is a causative agent of the disease visceral leishmaniasis, which can be fatal if not properly treated. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthesis pathways are attractive targets for new antileishmanial compounds since these Leishmania cell membrane phospholipids are important for parasite morphology and physiology. In this work we observed Leishmania synthesize PC and PE from extracellular choline and ethanolamine, respectively, suggesting the presence of CDP-choline and CDP-ethanolamine pathways. In addition, Leishmania converted PE to PC, indicating the parasite possesses phosphatidylethanolamine N-methyltransferase (PEMT) activity. The first step in the biosynthesis of PC or PE requires the phosphorylation of choline or ethanolamine by a kinase. We cloned the gene encoding a putative choline/ethanolamine kinase from Leishmania infantum and expressed and purified the encoded recombinant protein. The enzyme possesses choline kinase activity with a Vmax of 3.52μmol/min/mg and an apparent Km value of 0.089mM with respect to choline. The enzyme can also phosphorylate ethanolamine in vitro, but the apparent Km for ethanolamine is 850-fold greater than for choline. In an effort to probe requirements for small molecule inhibition of Leishmania choline kinase, the recombinant enzyme was evaluated for the ability to be inhibited by novel quaternary ammonium salts. The most effective inhibitor was N-iodomethyl-N,N,-dimethyl-N-(6,6-diphenyl hex-5-en-1-yle) ammonium iodide, denoted compound C6. In the presence of 4mM compound C6, the Vmax/Km decreased to approximately 1% of the wild-type catalytic efficiency. In addition, in Leishmania cells treated with compound C6 choline transport was inhibited.
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Affiliation(s)
- Sergio A Pulido
- Program for Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellin, Colombia
| | - Victoria H Nguyen
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA
| | - Juan F Alzate
- Parasitology Group, School of Medicine, University of Antioquia, Medellin, Colombia
| | - David L Cedeño
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA
| | - Monika A Makurath
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA
| | | | | | - Marjorie A Jones
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA
| | - Sara M Robledo
- Program for Study and Control of Tropical Diseases-PECET, School of Medicine, University of Antioquia, Medellin, Colombia
| | - Jon A Friesen
- Department of Chemistry, Illinois State University, Normal, IL 61790, USA.
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11
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Nectrisine Biosynthesis Genes in Thelonectria discophora SANK 18292: Identification and Functional Analysis. Appl Environ Microbiol 2016; 82:6414-6422. [PMID: 27565616 DOI: 10.1128/aem.01709-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/17/2016] [Indexed: 12/23/2022] Open
Abstract
The fungus Thelonectria discophora SANK 18292 produces the iminosugar nectrisine, which has a nitrogen-containing heterocyclic 5-membered ring and acts as a glycosidase inhibitor. In our previous study, an oxidase (designated NecC) that converts 4-amino-4-deoxyarabinitol to nectrisine was purified from T. discophora cultures. However, the genes required for nectrisine biosynthesis remained unclear. In this study, the nectrisine biosynthetic gene cluster in T. discophora was identified from the contiguous genome sequence around the necC gene. Gene disruption and complementation studies and heterologous expression of the gene showed that necA, necB, and necC could be involved in nectrisine biosynthesis, during which amination, dephosphorylation, and oxidation occur. It was also demonstrated that nectrisine could be produced by recombinant Escherichia coli coexpressing the necA, necB, and necC genes. These findings provide the foundation to develop a bacterial production system for nectrisine or its intermediates through genetic engineering. IMPORTANCE Iminosugars might have great therapeutic potential for treatment of many diseases. However, information on the genes for their biosynthesis is limited. In this study, we report the identification of genes required for biosynthesis of the iminosugar nectrisine in Thelonectria discophora SANK 18292, which was verified by disruption, complementation, and heterologous expression of the genes involved. We also demonstrate heterologous production of nectrisine by recombinant E. coli, toward developing an efficient production system for nectrisine or its intermediates through genetic engineering.
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12
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Arlauckas SP, Popov AV, Delikatny EJ. Choline kinase alpha-Putting the ChoK-hold on tumor metabolism. Prog Lipid Res 2016; 63:28-40. [PMID: 27073147 PMCID: PMC5360181 DOI: 10.1016/j.plipres.2016.03.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/14/2016] [Accepted: 03/26/2016] [Indexed: 12/24/2022]
Abstract
It is well established that lipid metabolism is drastically altered during tumor development and response to therapy. Choline kinase alpha (ChoKα) is a key mediator of these changes, as it represents the first committed step in the Kennedy pathway of phosphatidylcholine biosynthesis and ChoKα expression is upregulated in many human cancers. ChoKα activity is associated with drug resistant, metastatic, and malignant phenotypes, and represents a robust biomarker and therapeutic target in cancer. Effective ChoKα inhibitors have been developed and have recently entered clinical trials. ChoKα's clinical relevance was, until recently, attributed solely to its production of second messenger intermediates of phospholipid synthesis. The recent discovery of a non-catalytic scaffolding function of ChoKα may link growth receptor signaling to lipid biogenesis and requires a reinterpretation of the design and validation of ChoKα inhibitors. Advances in positron emission tomography, magnetic resonance spectroscopy, and optical imaging methods now allow for a comprehensive understanding of ChoKα expression and activity in vivo. We will review the current understanding of ChoKα metabolism, its role in tumor biology and the development and validation of targeted therapies and companion diagnostics for this important regulatory enzyme. This comes at a critical time as ChoKα-targeting programs receive more clinical interest.
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Affiliation(s)
- Sean P Arlauckas
- Department of Radiology, 317 Anatomy-Chemistry Building, 3620 Hamilton Walk, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anatoliy V Popov
- Department of Radiology, 317 Anatomy-Chemistry Building, 3620 Hamilton Walk, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E James Delikatny
- Department of Radiology, 317 Anatomy-Chemistry Building, 3620 Hamilton Walk, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Caldwell SJ, Huang Y, Berghuis AM. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2″)-Ia. Structure 2016; 24:935-45. [PMID: 27161980 DOI: 10.1016/j.str.2016.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 04/04/2016] [Indexed: 11/28/2022]
Abstract
APH(2″)-Ia is a widely disseminated resistance factor frequently found in clinical isolates of Staphylococcus aureus and pathogenic enterococci, where it is constitutively expressed. APH(2″)-Ia confers high-level resistance to gentamicin and related aminoglycosides through phosphorylation of the antibiotic using guanosine triphosphate (GTP) as phosphate donor. We have determined crystal structures of the APH(2″)-Ia in complex with GTP analogs, guanosine diphosphate, and aminoglycosides. These structures collectively demonstrate that aminoglycoside binding to the GTP-bound kinase drives conformational changes that bring distant regions of the protein into contact. These changes in turn drive a switch of the triphosphate cofactor from an inactive, stabilized conformation to a catalytically competent active conformation. This switch has not been previously reported for antibiotic kinases or for the structurally related eukaryotic protein kinases. This catalytic triphosphate switch presents a means by which the enzyme can curtail wasteful hydrolysis of GTP in the absence of aminoglycosides, providing an evolutionary advantage to this enzyme.
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Affiliation(s)
- Shane J Caldwell
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Yue Huang
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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14
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Design, synthesis, crystallization and biological evaluation of new symmetrical biscationic compounds as selective inhibitors of human Choline Kinase α1 (ChoKα1). Sci Rep 2016; 6:23793. [PMID: 27029499 PMCID: PMC4814829 DOI: 10.1038/srep23793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/14/2016] [Indexed: 01/20/2023] Open
Abstract
A novel family of compounds derivative of 1,1′-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))-bispyridinium or –bisquinolinium bromide (10a-l) containing a pair of oxygen atoms in the spacer of the linker between the biscationic moieties, were synthesized and evaluated as inhibitors of choline kinase against a panel of cancer-cell lines. The most promising compounds in this series were 1,1′-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))bis(4-(dimethylamino)pyridinium) bromide (10a) and 1,1′-(((ethane-1,2-diylbis(oxy))bis(4,1-phenylene))bis(methylene))-bis(7-chloro-4-(pyrrolidin-1-yl)quinolinium) bromide (10l), which inhibit human choline kinase (ChoKα1) with IC50 of 1.0 and 0.92 μM, respectively, in a range similar to that of the previously reported biscationic compounds MN58b and RSM932A. Our compounds show greater antiproliferative activities than do the reference compounds, with unprecedented values of GI50 in the nanomolar range for several of the cancer-cell lines assayed, and more importantly they present low toxicity in non-tumoral cell lines, suggesting a cancer-cell-selective antiproliferative activity. Docking studies predict that the compounds interact with the choline-binding site in agreement with the binding mode of most previously reported biscationic compounds. Moreover, the crystal structure of ChoKα1 with compound 10a reveals that this compound binds to the choline-binding site and mimics HC-3 binding mode as never before.
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15
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Design strategies, structure activity relationship and mechanistic insights for purines as kinase inhibitors. Eur J Med Chem 2016; 112:298-346. [PMID: 26907156 DOI: 10.1016/j.ejmech.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
Kinases control a diverse set of cellular processes comprising of reversible phosphorylation of proteins. Protein kinases play a pivotal role in human tumor cell proliferation, migration and survival of neoplasia. In the recent past, purine based molecules have emerged as significantly potent kinase inhibitors. In view of their promising potential for the inhibition of kinases, this review article focuses on purines which have progressed as kinase inhibitors during the last five years. A detailed account of the design strategies employed for the synthesis of purine analogs exerting inhibitory effects on diverse kinases has been presented. Apart from presenting the design strategies, the article also highlights the structure activity relationship along with mechanistic insights revealed during the biological evaluation of the purine analogs for kinase inhibition. The interactions with the amino acid residues responsible for kinase inhibitory potential of purine based molecules have also been discussed. In this assemblage, purine based protein kinase inhibitors patented in the past have also been summarized in the tabular form. This compilation will be of great interest for the researchers working in the area of protein kinase inhibitors.
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16
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Lai S, Safaei J, Pelech S. Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases. J Biol Chem 2016; 291:5199-205. [PMID: 26742849 DOI: 10.1074/jbc.m115.691428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 12/30/2022] Open
Abstract
The reversible phosphorylation of proteins catalyzed by protein kinases in eukaryotes supports an important role for eukaryotic protein kinases (ePKs) in the emergence of nucleated cells in the third superkingdom of life. Choline kinases (ChKs) could also be critical in the early evolution of eukaryotes, because of their function in the biosynthesis of phosphatidylcholine, which is unique to eukaryotic membranes. However, the genomic origins of ePKs and ChKs are unclear. The high degeneracy of protein sequences and broad expansion of ePK families have made this fundamental question difficult to answer. In this study, we identified two class-I aminoacyl-tRNA synthetases with high similarities to consensus amino acid sequences of human protein-serine/threonine kinases. Comparisons of primary and tertiary structures supported that ePKs and ChKs evolved from a common ancestor related to glutaminyl aminoacyl-tRNA synthetases, which may have been one of the key factors in the successful of emergence of ancient eukaryotic cells from bacterial colonies.
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Affiliation(s)
- Shenshen Lai
- From the Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5
| | - Javad Safaei
- the Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4, and
| | - Steven Pelech
- From the Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, the Kinexus Bioinformatics Corporation, Vancouver, British Columbia V6P 6T3, Canada
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17
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Oruganty K, Talevich EE, Neuwald AF, Kannan N. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol 2016; 16:7. [PMID: 26738562 PMCID: PMC4702295 DOI: 10.1186/s12862-015-0576-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (ELKs) share the same overall structural fold as EPKs, but differ in their modes of regulation, substrate recognition and specificity-the sequence and structural determinants of which are poorly understood. RESULTS To better understand the basis for ELK specificity, we applied a Bayesian classification procedure designed to identify sequence determinants responsible for functional divergence. This reveals that a large and diverse family of aminoglycoside kinases, characterized members of which are involved in antibiotic resistance, fall into major sub-groups based on differences in putative substrate recognition motifs. Aminoglycoside kinase substrate specificity follows simple rules of alternating hydroxyl and amino groups that is strongly correlated with variations at the DFG + 1 position. CONCLUSIONS Substrate specificity determining features in small molecule kinases are mostly confined to the catalytic core and can be identified based on quantitative sequence and crystal structure comparisons.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Eric E Talevich
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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18
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Wang L, Jiang YL, Zhang JR, Zhou CZ, Chen Y. Structural and enzymatic characterization of the choline kinase LicA from Streptococcus pneumoniae. PLoS One 2015; 10:e0120467. [PMID: 25781969 PMCID: PMC4364537 DOI: 10.1371/journal.pone.0120467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/22/2015] [Indexed: 01/07/2023] Open
Abstract
LicA plays a key role in the cell-wall phosphorylcholine biosynthesis of Streptococcus pneumonia. Here we determined the crystal structures of apo-form LicA at 1.94 Å and two complex forms LicA-choline and LicA-AMP-MES, at 2.01 and 1.45 Å resolution, respectively. The overall structure adopts a canonical protein kinase-like fold, with the active site located in the crevice of the N- and C-terminal domains. The three structures present distinct poses of the active site, which undergoes an open-closed-open conformational change upon substrate binding and product release. The structure analyses combined with mutageneses and enzymatic assays enabled us to figure out the key residues for the choline kinase activity of LicA. In addition, structural comparison revealed the loop between helices α7 and α8 might modulate the substrate specificity and catalytic activity. These findings shed light on the structure and mechanism of the prokaryotic choline kinase LicA, and might direct the rational design of novel anti-pneumococcal drugs.
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Affiliation(s)
- Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People’s Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People’s Republic of China,* E-mail: (YLJ); (YC)
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, 100084, People’s Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People’s Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People’s Republic of China,* E-mail: (YLJ); (YC)
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19
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Homotypic dimerization of a maltose kinase for molecular scaffolding. Sci Rep 2014; 4:6418. [PMID: 25245657 PMCID: PMC4171701 DOI: 10.1038/srep06418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/08/2014] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) uses maltose-1-phosphate to synthesize α-glucans that make up the major component of its outer capsular layer. Maltose kinase (MaK) catalyzes phosphorylation of maltose. The molecular basis for this phosphorylation is currently not understood. Here, we describe the first crystal structure of MtbMaK refined to 2.4 Å resolution. The bi-modular architecture of MtbMaK reveals a remarkably unique N-lobe. An extended sheet protrudes into ligand binding pocket of an adjacent monomer and contributes residues critical for kinase activity. Structure of the complex of MtbMaK bound with maltose reveals that maltose binds in a shallow cavity of the C-lobe. Structural constraints permit phosphorylation of α-maltose only. Surprisingly, instead of a Gly-rich loop, MtbMaK employs 'EQS' loop to tether ATP. Notably, this loop is conserved across all MaK homologues. Structures of MtbMaK presented here unveil features that are markedly different from other kinases and support the scaffolding role proposed for this kinase.
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20
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Hudson CS, Knegtel RM, Brown K, Charlton PA, Pollard JR. Kinetic and mechanistic characterisation of Choline Kinase-α. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1107-16. [PMID: 23416529 DOI: 10.1016/j.bbapap.2013.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/01/2013] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
Choline Kinase is a key component of the Kennedy pathway that converts choline into a number of structural and signalling lipids that are essential for cell growth and survival. One member of the family, Choline Kinase-α (ChoKα) is frequently up-regulated in human cancers, and expression of ChoKα is sufficient to transform cells. Consequently ChoKα has been studied as a potential target for therapeutic agents in cancer research. Despite great interest in the enzyme, mechanistic studies have not been reported. In this study, a combination of initial velocity and product inhibition studies, together with the kinetic and structural characterisation of a novel ChoKα inhibitor is used to support a mechanism of action for human ChoKα. Substrate and inhibition kinetics are consistent with an iso double displacement mechanism, in which the γ-phosphate from ATP is transferred to choline in two distinct steps via a phospho-enzyme intermediate. Co-crystal structures, and existing site-specific mutation studies, support an important role for Asp306, in stabilising the phospho-enzyme intermediate. The kinetics also indicate a distinct kinetic (isomerisation) step associated with product release, which may be attributed to a conformational change in the protein to disrupt an interaction between Asp306 and the phosphocholine product, facilitating product release. This study describes a mechanism for ChoKα that is unusual amongst kinases, and highlights the availability of different enzyme states that can be exploited for drug discovery.
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21
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Oruganty K, Kannan N. Design principles underpinning the regulatory diversity of protein kinases. Philos Trans R Soc Lond B Biol Sci 2012; 367:2529-39. [PMID: 22889905 PMCID: PMC3415841 DOI: 10.1098/rstb.2012.0015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Protein phosphorylation in eukaryotes is carried out by a large and diverse family of protein kinases, which display remarkable diversity and complexity in their modes of regulation. The complex modes of regulation have evolved as a consequence of natural selection operating on protein kinase sequences for billions of years. Here we describe how quantitative comparisons of protein kinase sequences from diverse organisms, in particular prokaryotes, have contributed to our understanding of the structural organization and evolution of allosteric regulation in the protein kinase domain. An emerging view from these studies is that regulatory diversity and complexity in the protein kinase domain evolved in a ‘modular’ fashion through elaboration of an ancient core component, which existed before the emergence of eukaryotes. The core component provided the conformational flexibility required for ATP binding and phosphoryl transfer in prokaryotic kinases, but evolved into a highly regulatable domain in eukaryotes through the addition of exaggerated structural features that facilitated tight allosteric control. Family and group-specific features are built upon the core component in eukaryotes to provide additional layers of control. We propose that ‘modularity’ and ‘conformational flexibility’ are key evolvable traits of the protein kinase domain that contributed to its extensive regulatory diversity and complexity.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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22
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Taylor SS, Keshwani MM, Steichen JM, Kornev AP. Evolution of the eukaryotic protein kinases as dynamic molecular switches. Philos Trans R Soc Lond B Biol Sci 2012; 367:2517-28. [PMID: 22889904 PMCID: PMC3415842 DOI: 10.1098/rstb.2012.0054] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Protein kinases have evolved in eukaryotes to be highly dynamic molecular switches that regulate a plethora of biological processes. Two motifs, a dynamic activation segment and a GHI helical subdomain, distinguish the eukaryotic protein kinases (EPKs) from the more primitive eukaryotic-like kinases. The EPKs are themselves highly regulated, typically by phosphorylation, and this allows them to be rapidly turned on and off. The EPKs have a novel hydrophobic architecture that is typically regulated by the dynamic assembly of two hydrophobic spines that is usually mediated by the phosphorylation of an activation loop phosphate. Cyclic AMP-dependent protein kinase (protein kinase A (PKA)) is used as a prototype to exemplify these features of the PKA superfamily. Specificity in PKA signalling is achieved in large part by packaging the enzyme as inactive tetrameric holoenzymes with regulatory subunits that then are localized to macromolecular complexes in close proximity to dedicated substrates by targeting scaffold proteins. In this way, the cell creates discrete foci that most likely represent the physiological environment for cyclic AMP-mediated signalling.
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Affiliation(s)
- Susan S Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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23
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Phosphatidylcholine and the CDP-choline cycle. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1831:523-32. [PMID: 23010477 DOI: 10.1016/j.bbalip.2012.09.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/16/2012] [Indexed: 11/20/2022]
Abstract
The CDP-choline pathway of phosphatidylcholine (PtdCho) biosynthesis was first described more than 50 years ago. Investigation of the CDP-choline pathway in yeast provides a basis for understanding the CDP-choline pathway in mammals. PtdCho is considered as an intermediate in a cycle of synthesis and degradation, and the activity of a CDP-choline cycle is linked to subcellular membrane lipid movement. The components of the mammalian CDP-choline pathway include choline transport, choline kinase, phosphocholine cytidylyltransferase, and choline phosphotransferase activities. The protein isoforms and biochemical mechanisms of regulation of the pathway enzymes are related to their cell- and tissue-specific functions. Regulated PtdCho turnover mediated by phospholipases or neuropathy target esterase participates in the mammalian CDP-choline cycle. Knockout mouse models define the biological functions of the CDP-choline cycle in mammalian cells and tissues. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.
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24
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Rubio-Ruíz B, Conejo-García A, Ríos-Marco P, Carrasco-Jiménez MP, Segovia J, Marco C, Gallo MA, Espinosa A, Entrena A. Design, synthesis, theoretical calculations and biological evaluation of new non-symmetrical choline kinase inhibitors. Eur J Med Chem 2012; 50:154-62. [PMID: 22348828 DOI: 10.1016/j.ejmech.2012.01.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 01/17/2012] [Accepted: 01/24/2012] [Indexed: 01/03/2023]
Abstract
Inhibition of Choline Kinase (ChoK) has been reported as a therapeutical target in the treatment of some kinds of tumor. In this paper, the design and synthesis of new non-symmetrical monocationic ChoK inhibitors is described, bearing a cationic head and an adenine moiety connected by linkers of different lengths. Docking studies indicate that the cationic head of these compounds could be inserted into the choline binding site of the enzyme, while the adenine moiety could be stabilized into the ATP binding site. Docking studies also support the difference of activity of the synthesized compounds, which depends on both the substituent at position 4 of the cationic head and the linker length, being dimethylamine and 1,4-diphenylbutane respectively, the most appropriate ones. Compounds 14 (IC(50) = 10.70 ± 0.40 μM) and 17 (IC(50) = 6.21 ± 0.97 μM) are the most potent ChoK inhibitors and suitable for further modification with a view to obtain more potent antitumor compounds.
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Affiliation(s)
- Belén Rubio-Ruíz
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Campus de Cartuja, 18071 Granada, Spain
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25
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Abstract
The yeast Saccharomyces cerevisiae, with its full complement of organelles, synthesizes membrane phospholipids by pathways that are generally common to those found in higher eukaryotes. Phospholipid synthesis in yeast is regulated in response to a variety of growth conditions (e.g., inositol supplementation, zinc depletion, and growth stage) by a coordination of genetic (e.g., transcriptional activation and repression) and biochemical (e.g., activity modulation and localization) mechanisms. Phosphatidate (PA), whose cellular levels are controlled by the activities of key phospholipid synthesis enzymes, plays a central role in the transcriptional regulation of phospholipid synthesis genes. In addition to the regulation of gene expression, phosphorylation of key phospholipid synthesis catalytic and regulatory proteins controls the metabolism of phospholipid precursors and products.
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Affiliation(s)
- George M Carman
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey 08901, USA.
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26
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Miyake T, Parsons SJ. Functional interactions between Choline kinase α, epidermal growth factor receptor and c-Src in breast cancer cell proliferation. Oncogene 2011; 31:1431-41. [PMID: 21822308 PMCID: PMC3213328 DOI: 10.1038/onc.2011.332] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Epidermal growth factor receptor (EGFR) family members and c-Src are co-overexpressed in many cancers. The synergistic effect of EGFR and c-Src has been shown in the tumorigenesis of breast and other cancers. Reported mechanisms of synergy include transcriptional regulation by STAT5b and the regulation of cellular ATP production by mitochondrial protein COX II. Here, we report a new mechanism of EGFR-c-Src synergy through choline kinase α (CHKA). The first enzyme of the phosphatidyl choline production pathway, CHKA, is overexpressed in many cancers, and the product of the enzyme, phosphocholine, is also increased in tumor cells. In this report, we find that CHKA forms a complex with EGFR in a c-Src-dependent manner. Endogenous CHKA and EGFR co-immunoprecipitated from a variety of breast cancer cell lines and immortalized mammary epithelial cells. CHKA interacted with the EGFR kinase domain upon c-Src co-overexpression and was phosphorylated in a c-Src-dependent manner on Y197 and Y333. Overexpression of EGFR and c-Src increased total cellular activity and protein levels of CHKA. Mutation of CHKA Y197 and Y333 reduced complex formation, EGFR-dependent activation of CHKA enzyme activity and epidermal growth factor (EGF)-dependent DNA synthesis. Furthermore, small interfering RNA-mediated knockdown of CHKA in MCF-7 and MCF-10A cells reduced EGF-dependent cell proliferation. Together, these results strongly implicate a new c-Src-dependent link between CHKA and EGFR, which contributes to the regulation of cell proliferation and tumorigenesis.
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Affiliation(s)
- T Miyake
- Department of Microbiology and Cancer Center, University of Virginia Health System, Charlottesville, VA, USA
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27
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Affiliation(s)
- Mariya Morar
- M.G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada;
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada;
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28
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Scheeff ED, Axelrod HL, Miller MD, Chiu HJ, Deacon AM, Wilson IA, Manning G. Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. Proteins 2010; 78:1470-82. [PMID: 20077512 PMCID: PMC2860764 DOI: 10.1002/prot.22663] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacterial spore formation is a complex process of fundamental relevance to biology and human disease. The spore coat structure is complex and poorly understood, and the roles of many of the protein components remain unclear. We describe a new family of spore coat proteins, the bacterial spore kinases (BSKs), and the first crystal structure of a BSK, YtaA (CotI) from Bacillus subtilis. BSKs are widely distributed in spore-forming Bacillus and Clostridium species, and have a dynamic evolutionary history. Sequence and structure analyses indicate that the BSKs are CAKs, a prevalent group of small molecule kinases in bacteria that is distantly related to the eukaryotic protein kinases. YtaA has substantial structural similarity to CAKs, but also displays distinctive features that broaden our understanding of the CAK group. Evolutionary constraint analysis of the protein surfaces indicates that members of the BSK family have distinct clade-conserved patterns in the substrate binding region, and probably bind and phosphorylate distinct targets. Several classes of BSKs have apparently independently lost catalytic activity to become pseudokinases, indicating that the family also has a major noncatalytic function. Proteins 2010. © 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Eric D Scheeff
- Razavi Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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29
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Hong BS, Allali-Hassani A, Tempel W, Finerty PJ, MacKenzie F, Dimov S, Vedadi M, Park HW. Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity. J Biol Chem 2010; 285:16330-40. [PMID: 20299452 PMCID: PMC2871500 DOI: 10.1074/jbc.m109.039024] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 02/28/2010] [Indexed: 12/03/2022] Open
Abstract
Human choline kinase (ChoK) catalyzes the first reaction in phosphatidylcholine biosynthesis and exists as ChoKalpha (alpha1 and alpha2) and ChoKbeta isoforms. Recent studies suggest that ChoK is implicated in tumorigenesis and emerging as an attractive target for anticancer chemotherapy. To extend our understanding of the molecular mechanism of ChoK inhibition, we have determined the high resolution x-ray structures of the ChoKalpha1 and ChoKbeta isoforms in complex with hemicholinium-3 (HC-3), a known inhibitor of ChoK. In both structures, HC-3 bound at the conserved hydrophobic groove on the C-terminal lobe. One of the HC-3 oxazinium rings complexed with ChoKalpha1 occupied the choline-binding pocket, providing a structural explanation for its inhibitory action. Interestingly, the HC-3 molecule co-crystallized with ChoKbeta was phosphorylated in the choline binding site. This phosphorylation, albeit occurring at a very slow rate, was confirmed experimentally by mass spectroscopy and radioactive assays. Detailed kinetic studies revealed that HC-3 is a much more potent inhibitor for ChoKalpha isoforms (alpha1 and alpha2) compared with ChoKbeta. Mutational studies based on the structures of both inhibitor-bound ChoK complexes demonstrated that Leu-401 of ChoKalpha2 (equivalent to Leu-419 of ChoKalpha1), or the corresponding residue Phe-352 of ChoKbeta, which is one of the hydrophobic residues neighboring the active site, influences the plasticity of the HC-3-binding groove, thereby playing a key role in HC-3 sensitivity and phosphorylation.
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Affiliation(s)
| | | | | | | | | | | | | | - Hee-Won Park
- From the Structural Genomics Consortium and
- Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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Fong DH, Lemke CT, Hwang J, Xiong B, Berghuis AM. Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila. J Biol Chem 2010; 285:9545-9555. [PMID: 20089863 DOI: 10.1074/jbc.m109.038364] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoglycoside phosphotransferases (APHs) constitute a diverse group of enzymes that are often the underlying cause of aminoglycoside resistance in the clinical setting. Several APHs have been extensively characterized, including the elucidation of the three-dimensional structure of two APH(3') isozymes and an APH(2'') enzyme. Although many APHs are plasmid-encoded and are capable of inactivating numerous 2-deoxystreptmaine aminoglycosides with multiple regiospecificity, APH(9)-Ia, isolated from Legionella pneumophila, is an unusual enzyme among the APH family for its chromosomal origin and its specificity for a single non-2-deoxystreptamine aminoglycoside substrate, spectinomycin. We describe here the crystal structures of APH(9)-Ia in its apo form, its binary complex with the nucleotide, AMP, and its ternary complex bound with ADP and spectinomycin. The structures reveal that APH(9)-Ia adopts the bilobal protein kinase-fold, analogous to the APH(3') and APH(2'') enzymes. However, APH(9)-Ia differs significantly from the other two types of APH enzymes in its substrate binding area and that it undergoes a conformation change upon ligand binding. Moreover, kinetic assay experiments indicate that APH(9)-Ia has stringent substrate specificity as it is unable to phosphorylate substrates of choline kinase or methylthioribose kinase despite high structural resemblance. The crystal structures of APH(9)-Ia demonstrate and expand our understanding of the diversity of the APH family, which in turn will facilitate the development of new antibiotics and inhibitors.
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Affiliation(s)
- Desiree H Fong
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6
| | - Christopher T Lemke
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Jiyoung Hwang
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6
| | - Bing Xiong
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6; Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.
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31
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Comparison of the cellular and biochemical properties of Plasmodium falciparum choline and ethanolamine kinases. Biochem J 2009; 425:149-58. [PMID: 19845508 DOI: 10.1042/bj20091119] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The proliferation of the malaria-causing parasite Plasmodium falciparum within the erythrocyte is concomitant with massive phosphatidylcholine and phosphatidylethanolamine biosynthesis. Based on pharmacological and genetic data, de novo biosynthesis pathways of both phospholipids appear to be essential for parasite survival. The present study characterizes PfCK (P. falciparum choline kinase) and PfEK (P. falciparum ethanolamine kinase), which catalyse the first enzymatic steps of these essential metabolic pathways. Recombinant PfCK and PfEK were expressed as His6-tagged fusion proteins from overexpressing Escherichia coli strains, then purified to homogeneity and characterized. Using murine polyclonal antibodies against recombinant kinases, PfCK and PfEK were shown to be localized within the parasite cytoplasm. Protein expression levels increased during erythrocytic development. PfCK and PfEK appeared to be specific to their respective substrates and followed Michaelis-Menten kinetics. The Km value of PfCK for choline was 135.3+/-15.5 microM. PfCK was also able to phosphorylate ethanolamine with a very low affinity. PfEK was found to be an ethanolamine-specific kinase (Km=475.7+/-80.2 microM for ethanolamine). The quaternary ammonium compound hemicholinium-3 and an ethanolamine analogue, 2-amino-1-butanol, selectively inhibited PfCK or PfEK. In contrast, the bis-thiazolium compound T3, which was designed as a choline analogue and is currently in clinical trials for antimalarial treatment, affected PfCK and PfEK activities similarly. Inhibition exerted by T3 was competitive for both PfCK and PfEK and correlated with the impairment of cellular phosphatidylcholine biosynthesis. Comparative analyses of sequences and structures for both kinase types gave insights into their specific inhibition profiles and into the dual capacity of T3 to inhibit both PfCK and PfEK.
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32
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Sonobe H, Ito Y. Phosphoconjugation and dephosphorylation reactions of steroid hormone in insects. Mol Cell Endocrinol 2009; 307:25-35. [PMID: 19524123 DOI: 10.1016/j.mce.2009.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 03/23/2009] [Indexed: 10/21/2022]
Abstract
In insects, the major products of phase II metabolism of ecdysteroids, which include the molting hormone, are phosphate esters. The phosphoconjugation pathway is a reversible process, comprising two enzyme systems: ecdysteroid 22-kinase (EcKinase) and ecdysteroid-phosphate phosphatase (EPPase). We report here that: (1) the biochemical characteristics of EcKinase and EPPase, (2) the physiological significance of the reciprocal conversion of ecdysteroids and ecdysteroid phosphates in the ovary-egg system in insects, (3) the biochemical mechanism by which ecdysteroid phosphates are synthesized in the ovary, transferred to eggs, and finally dephosphorylated in eggs, and (4) the possible catalytic steps of EcKinase and EPPase on the basis of the data obtained by an in silico study. From these studies, it is obvious that ecdysteroid phosphates as well as steroid sulfates, which are major products of phase II metabolism in mammals, function as precursors for the formation of biologically active hormones.
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Affiliation(s)
- Haruyuki Sonobe
- Department of Biology, Konan University, Higashinada-ku, Kobe, Japan.
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Srivani P, Sastry GN. Potential choline kinase inhibitors: a molecular modeling study of bis-quinolinium compounds. J Mol Graph Model 2008; 27:676-88. [PMID: 19147382 DOI: 10.1016/j.jmgm.2008.10.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 10/10/2008] [Accepted: 10/27/2008] [Indexed: 11/19/2022]
Abstract
Choline kinase (ChoK) is reported to involve in cell signaling pathways and cell growth by regulating the intermediate, phosphocholine (PCho), which is the first step to biosynthesis a membrane phospholipid, phosphatidylcholine. The PCho levels are overexpressed due to elevated activation of the protein under carcinogenesis conditions. ChoK has thus evolved as a novel target for various cancers and a range of compounds has been reported in this course as potent ChoK inhibitors. However, not much information is known about the binding site of the inhibitors. Therefore, we ventured to unravel the possible binding site of 39 bis-quinolinium inhibitors from which the structural requirement for better protein-ligand complex was delved. Molecular docking and 3D-QSAR studies namely comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on the series. The knowledge of the active site was obtained from the site id search and molcad surface calculations of Sybyl, which was further considered for docking studies. In 3D-QSAR, the best predictions were obtained from the model where 29 compounds were considered in the training set and remaining 10 in the test set. The best CoMFA statistics were obtained with r(2) of 0.99 and q(2) of 0.81 while, CoMSIA was resulted with r(2) of 0.98 and q(2) of 0.77. A comparative analysis was done with the resulted 3D-QSAR maps and the docked poses by overlaying the maps on the active site residues. Since, there is no reported ligand co-crystallized structure of ChoK the present study provides valuable clues on the binding conformation of the ligand and its interactions with the active site.
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Affiliation(s)
- P Srivani
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India
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34
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Biochemical characterization of the initial steps of the Kennedy pathway in Trypanosoma brucei: the ethanolamine and choline kinases. Biochem J 2008; 415:135-44. [PMID: 18489261 PMCID: PMC2552378 DOI: 10.1042/bj20080435] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ethanolamine and choline are major components of the trypanosome membrane phospholipids, in the form of GPEtn (glycerophosphoethanolamine) and GPCho (glycerophosphocholine). Ethanolamine is also found as an integral component of the GPI (glycosylphosphatidylinositol) anchor that is required for membrane attachment of cell-surface proteins, most notably the variant-surface glycoproteins. The de novo synthesis of GPEtn and GPCho starts with the generation of phosphoethanolamine and phosphocholine by ethanolamine and choline kinases via the Kennedy pathway. Database mining revealed two putative C/EKs (choline/ethanolamine kinases) in the Trypanosoma brucei genome, which were cloned, overexpressed, purified and characterized. TbEK1 (T. brucei ethanolamine kinase 1) was shown to be catalytically active as an ethanolamine-specific kinase, i.e. it had no choline kinase activity. The Km values for ethanolamine and ATP were found to be 18.4±0.9 and 219±29 μM respectively. TbC/EK2 (T. brucei choline/ethanolamine kinase 2), on the other hand, was found to be able to phosphorylate both ethanolamine and choline, even though choline was the preferred substrate, with a Km 80 times lower than that of ethanolamine. The Km values for choline, ethanolamine and ATP were 31.4±2.6 μM, 2.56±0.31 mM and 20.6±1.96 μM respectively. Further substrate specificity analysis revealed that both TbEK1 and TbC/EK2 were able to tolerate various modifications at the amino group, with the exception of a quaternary amine for TbEK1 (choline) and a primary amine for TbC/EK2 (ethanolamine). Both enzymes recognized analogues with substituents on C-2, but substitutions on C-1 and elongations of the carbon chain were not well tolerated.
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35
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Ku SY, Cornell KA, Howell PL. Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog. BMC STRUCTURAL BIOLOGY 2007; 7:70. [PMID: 17961230 PMCID: PMC2194712 DOI: 10.1186/1472-6807-7-70] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 10/25/2007] [Indexed: 11/30/2022]
Abstract
Background Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics. Results The structure of Arabidopsis thaliana MTR kinase co-crystallized with ATPγS and MTR has been determined at 1.9 Å resolution. The structure is similar to B. subtilis MTR kinase and has the same protein kinase fold observed in other evolutionarily related protein kinase-like phosphotransferases. The active site is comparable between the two enzymes with the DXE-motif coordinating the nucleotide-Mg, the D238 of the HGD catalytic loop polarizing the MTR O1 oxygen, and the RR-motif interacting with the substrate MTR. Unlike its bacterial homolog, however, the Gly-rich loop (G-loop) of A. thaliana MTR kinase has an extended conformation, which shields most of the active site from solvent, a feature that resembles eukaryotic protein kinases more than the bacterial enzyme. The G- and W-loops of A. thaliana and B. subtilis MTR kinase adopt different conformations despite high sequence similarity. The ATPγS analog was hydrolyzed during the co-crystallization procedure, resulting in ADP in the active site. This suggests that the A. thaliana enzyme, like its bacterial homolog, may have significant ATPase activity in the absence of MTR. Conclusion The structure of A. thaliana MTR kinase provides a template for structure-based design of agrochemicals, particularly herbicides whose effectiveness could be regulated by nutrient levels. Features of the MTR binding site offer an opportunity for a simple organic salt of an MTR analog to specifically inhibit MTR kinase.
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Affiliation(s)
- Shao-Yang Ku
- Program in Molecular Structure and Function, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, CANADA.
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36
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Zheng J, He C, Singh VK, Martin NL, Jia Z. Crystal structure of a novel prokaryotic Ser/Thr kinase and its implication in the Cpx stress response pathway. Mol Microbiol 2007; 63:1360-71. [PMID: 17302814 DOI: 10.1111/j.1365-2958.2007.05611.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Cpx signalling system of Escherichia coli and Salmonella enterica senses extracytoplasmic stress and controls expression of factors that allow the bacterium to adapt to these stressors and thereby enhance survival. Many of the Cpx-responsive genes products are of unknown function. We determined the crystal structure of one of these gene products, called YihE in E. coli, which exhibits a eukaryotic kinase fold. Functional assays established that both YihE and the S. enterica YihE homologue, RdoA, undergo autophosphorylation and phosphorylate protein substrates at Ser/Thr residues in vitro, demonstrating that YihE/RdoA is a novel Ser/Thr protein kinase in prokaryotic cells. Phenotypic analysis of yihE/rdoA null strains indicates that this kinase is most abundant in stationary phase, and is important for long-term cell survival and for expression of surface appendages in both a Cpx-independent and -dependent manner. YihE/RdoA is therefore a previously unknown kinase component of a new type of bacterial phosphorelay mechanism, adding kinase activity as another response to the Cpx sensing system that functions to maintain cellular homeostasis.
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Affiliation(s)
- Jimin Zheng
- Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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37
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Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G. Structural and functional diversity of the microbial kinome. PLoS Biol 2007; 5:e17. [PMID: 17355172 PMCID: PMC1821047 DOI: 10.1371/journal.pbio.0050017] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 09/20/2006] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic protein kinase (ePK) domain mediates the majority of signaling and coordination of complex events in eukaryotes. By contrast, most bacterial signaling is thought to occur through structurally unrelated histidine kinases, though some ePK-like kinases (ELKs) and small molecule kinases are known in bacteria. Our analysis of the Global Ocean Sampling (GOS) dataset reveals that ELKs are as prevalent as histidine kinases and may play an equally important role in prokaryotic behavior. By combining GOS and public databases, we show that the ePK is just one subset of a diverse superfamily of enzymes built on a common protein kinase-like (PKL) fold. We explored this huge phylogenetic and functional space to cast light on the ancient evolution of this superfamily, its mechanistic core, and the structural basis for its observed diversity. We cataloged 27,677 ePKs and 18,699 ELKs, and classified them into 20 highly distinct families whose known members suggest regulatory functions. GOS data more than tripled the count of ELK sequences and enabled the discovery of novel families and classification and analysis of all ELKs. Comparison between and within families revealed ten key residues that are highly conserved across families. However, all but one of the ten residues has been eliminated in one family or another, indicating great functional plasticity. We show that loss of a catalytic lysine in two families is compensated by distinct mechanisms both involving other key motifs. This diverse superfamily serves as a model for further structural and functional analysis of enzyme evolution.
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Affiliation(s)
- Natarajan Kannan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Yufeng Zhai
- Razavi-Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - J. Craig Venter
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Gerard Manning
- Razavi-Newman Center for Bioinformatics, Salk Institute for Biological Studies, La Jolla, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Aoyama C, Ishidate K, Sugimoto H, Vance DE. Induction of choline kinase alpha by carbon tetrachloride (CCl4) occurs via increased binding of c-jun to an AP-1 element. Biochim Biophys Acta Mol Cell Biol Lipids 2007; 1771:1148-55. [PMID: 17728180 DOI: 10.1016/j.bbalip.2007.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 06/30/2007] [Accepted: 07/14/2007] [Indexed: 10/23/2022]
Abstract
The mechanism by which treatment of mice with CCl4 induces an increase in choline kinase alpha has been investigated. Nuclear run on assays demonstrated a major increase in the transcript for choline kinase alpha in livers from mice 3 h and 6 h after administration of CCl4 compared to vehicle (olive oil). 5'deletion analyses of choline kinase alpha promoter-luciferase constructs expressed in Hepa-1 cells identified a promoter element between -875 and -866 that was nearly identical to an AP-1 consensus site. Mutation of this AP-1 site caused a striking decrease in the expression of choline kinase alpha promoter-luciferase constructs. Electromobility shift assays with nuclear extracts from mouse liver demonstrated that c-Jun, but not c-fos, bound oligonucleotides with the AP-1 site. The amount of c-jun bound was greatly increased when hepatic nuclear extracts from mice treated with CCl4 were used. Chromatin immunoprecipitation assays confirmed that c-jun binds to the choline kinase alpha promoter. The results from these studies provide strong evidence that the choline kinase alpha promoter has a distal element (-875/-867) that binds c-jun and the binding of c-jun is enhanced by treatment with CCl4.
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Affiliation(s)
- Chieko Aoyama
- Department of Biochemistry and the Canadian Institutes of Health Research Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada T6G 2S2.
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Ku SY, Yip P, Cornell KA, Riscoe MK, Behr JB, Guillerm G, Howell PL. Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding. J Biol Chem 2007; 282:22195-206. [PMID: 17522047 DOI: 10.1074/jbc.m611045200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The methionine salvage pathway is ubiquitous in all organisms, but metabolic variations exist between bacteria and mammals. 5-Methylthioribose (MTR) kinase is a key enzyme in methionine salvage in bacteria and the absence of a mammalian homolog suggests that it is a good target for the design of novel antibiotics. The structures of the apo-form of Bacillus subtilis MTR kinase, as well as its ADP, ADP-PO(4), AMPPCP, and AMPPCP-MTR complexes have been determined. MTR kinase has a bilobal eukaryotic protein kinase fold but exhibits a number of unique features. The protein lacks the DFG motif typically found at the beginning of the activation loop and instead coordinates magnesium via a DXE motif (Asp(250)-Glu(252)). In addition, the glycine-rich loop of the protein, analogous to the "Gly triad" in protein kinases, does not interact extensively with the nucleotide. The MTR substrate-binding site consists of Asp(233) of the catalytic HGD motif, a novel twin arginine motif (Arg(340)/Arg(341)), and a semi-conserved W-loop, which appears to regulate MTR binding specificity. No lobe closure is observed for MTR kinase upon substrate binding. This is probably because the enzyme lacks the lobe closure/inducing interactions between the C-lobe of the protein and the ribosyl moiety of the nucleotide that are typically responsible for lobe closure in protein kinases. The current structures suggest that MTR kinase has a dissociative mechanism.
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Affiliation(s)
- Shao-Yang Ku
- Program in Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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40
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Milanese L, Espinosa A, Campos JM, Gallo MA, Entrena A. Insight into the inhibition of human choline kinase: homology modeling and molecular dynamics simulations. ChemMedChem 2007; 1:1216-28. [PMID: 17009359 DOI: 10.1002/cmdc.200600158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A homology model of human choline kinase (CK-alpha) based on the X-ray crystallographic structure of C. elegans choline kinase (CKA-2) is presented. Molecular dynamics simulations performed on CK-alpha confirm the quality of the model, and also support the putative ATP and choline binding sites. A good correlation between the MD results and reported CKA-2 mutagenesis assays has been found for the main residues involved in catalytic activity. Preliminary docking studies performed on the CK-alpha model indicate that inhibitors can bind to the binding sites of both substrates (ATP and choline). A possible reason for inhibition of choline kinase by Ca(2+) ion is also proposed.
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Affiliation(s)
- Lara Milanese
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Campus de Cartuja s/n, Universidad de Granada, 18071 Granada, Spain
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41
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Malito E, Sekulic N, Too WCS, Konrad M, Lavie A. Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine. J Mol Biol 2006; 364:136-51. [PMID: 17007874 PMCID: PMC1885479 DOI: 10.1016/j.jmb.2006.08.084] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 08/25/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
Abstract
Choline kinase, responsible for the phosphorylation of choline to phosphocholine as the first step of the CDP-choline pathway for the biosynthesis of phosphatidylcholine, has been recognized as a new target for anticancer therapy. Crystal structures of human choline kinase in its apo, ADP and phosphocholine-bound complexes, respectively, reveal the molecular details of the substrate binding sites. ATP binds in a cavity where residues from both the N and C-terminal lobes contribute to form a cleft, while the choline-binding site constitutes a deep hydrophobic groove in the C-terminal domain with a rim composed of negatively charged residues. Upon binding of choline, the enzyme undergoes conformational changes independently affecting the N-terminal domain and the ATP-binding loop. From this structural analysis and comparison with other kinases, and from mutagenesis data on the homologous Caenorhabditis elegans choline kinase, a model of the ternary ADP.phosphocholine complex was built that reveals the molecular basis for the phosphoryl transfer activity of this enzyme.
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Affiliation(s)
- Enrico Malito
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, 60607
| | - Nikolina Sekulic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, 60607
| | - Wei Cun See Too
- Department of Molecular Genetics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany, D-37077
| | - Manfred Konrad
- Department of Molecular Genetics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany, D-37077
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, 60607
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42
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Tian Y, Jackson P, Gunter C, Wang J, Rock CO, Jackowski S. Placental thrombosis and spontaneous fetal death in mice deficient in ethanolamine kinase 2. J Biol Chem 2006; 281:28438-49. [PMID: 16861741 DOI: 10.1074/jbc.m605861200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ethanolamine kinase catalyzes the first step in the CDP-ethanolamine pathway for the formation of the major membrane phospholipid phosphatidylethanolamine (PtdEtn). In this work, the predicted Etnk2 cDNA was established as a soluble protein with ethanolamine-specific kinase activity that was most highly expressed in liver. Mice with an inactivated Etnk2 gene were derived, and its absence reduced the rate of PtdEtn synthesis from exogenous ethanolamine in hepatocytes. PtdEtn is a major precursor to phosphatidylcholine in liver; however, Etnk2(-/-) mice did not have reduced amounts of either PtdEtn or phosphatidylcholine or an altered phospholipid molecular species distribution. The knock-out animals were able to adapt to a choline-deficient diet. The Etnk2(-/-) mice exhibited a maternal-specific intrauterine growth retardation phenotype that resulted in a 33% reduction in litter size and frequent perinatal death. Histological analysis of pregnant Etnk2(-/-) females showed that fetal development failed at the late stage of pregnancy in a significant percentage of embryos because of the appearance of extensive placental thrombosis. These results illustrate a non-redundant role for EtnK2 expression in regulating placental hemostasis.
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Affiliation(s)
- Yong Tian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
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43
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Sonobe H, Ohira T, Ieki K, Maeda S, Ito Y, Ajimura M, Mita K, Matsumoto H, Wilder MN. Purification, kinetic characterization, and molecular cloning of a novel enzyme, ecdysteroid 22-kinase. J Biol Chem 2006; 281:29513-24. [PMID: 16899460 DOI: 10.1074/jbc.m604035200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This is the first report succeeding in the isolation and characterization of an enzyme and its gene involved in the phosphorylation of a steroid hormone. It has been demonstrated that ecdysteroid 22-phosphates in insect ovaries, which are physiologically inactive, serve as a "reservoir" that supplies active free ecdysteroids during early embryonic development and that their dephosphorylation is catalyzed by a specific enzyme, ecdysteroid-phosphate phosphatase (Yamada, R., and Sonobe, H. (2003), J. Biol. Chem. 278, 26365-26373). In this study, ecdysteroid 22-kinase (EcKinase) was purified from the cytosol of the silkworm Bombyx mori ovaries to about 1,800-fold homogeneity in six steps of column chromatography and biochemically characterized. Results obtained indicated that the reciprocal conversion of free ecdysteroids and ecdysteroid 22-phosphates by two enzymes, EcKinase and ecdysteroid-phosphate phosphatase, plays an important role in ecdysteroid economy of the ovary-egg system of B. mori. On the basis of the partial amino acid sequence obtained from purified EcKinase, the nucleotide sequence of the cDNA encoding EcKinase was determined. The full-length cDNA of EcKinase was composed of 1,850 bp with an open reading frame encoding a protein of 386 amino acid residues. The cloned cDNA was confirmed to encode the functional EcKinase using the transformant harboring the open reading frame of EcKinase. A data base search showed that EcKinase has an amino acid sequence characteristic of phosphotransferases, in that it harbors Brenner's motif and putative ATP binding sites, but there are no functional proteins that share high identity with the amino acid sequence of EcKinase.
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Affiliation(s)
- Haruyuki Sonobe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan.
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Choubey V, Guha M, Maity P, Kumar S, Raghunandan R, Maulik PR, Mitra K, Halder UC, Bandyopadhyay U. Molecular characterization and localization of Plasmodium falciparum choline kinase. Biochim Biophys Acta Gen Subj 2006; 1760:1027-38. [PMID: 16626864 DOI: 10.1016/j.bbagen.2006.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 02/24/2006] [Accepted: 03/01/2006] [Indexed: 10/24/2022]
Abstract
Generation of phosphocholine by choline kinase is important for phosphatidylcholine biosynthesis via Kennedy pathway and phosphatidylcholine biosynthesis is essential for intraerythrocytic growth of malaria parasite. A putative gene (Gene ID PF14_0020) in chromosome 14, having highest sequence homology with choline kinase, has been identified by BLAST searches from P. falciparum genome sequence database. This gene has been PCR amplified, cloned, over-expressed and characterized. Choline kinase activity of the recombinant protein (PfCK) was validated as it catalyzed the formation of phosphocholine from choline in presence of ATP. The K(m) values for choline and ATP are found to be 145+/-20 microM and 2.5+/-0.3 mM, respectively. PfCK can phosphorylate choline efficiently but not ethanolamine. Southern blotting indicates that PfCK is a single copy gene and it is a cytosolic protein as evidenced by Western immunoblotting and confocal microscopy. A model structure of PfCK was constructed based on the crystal structure of choline kinase of C. elegans to search the structural homology. Consistent with the homology modeling predictions, CD analysis indicates that the alpha and beta content of PfCK are 33% and 14%, respectively. Since choline kinase plays a vital role for growth and multiplication of P. falciparum during intraerythrocytic stages, we can suggest that this well characterized PfCK may be exploited in the screening of new choline kinase inhibitors to evaluate their antimalarial activity.
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Affiliation(s)
- Vinay Choubey
- Division of Drug Target Discovery and Development, Central Drug Research Institute, Chatter Manzil Palace, Mahatma Gandhi Marg, Lucknow-226001, Uttar Pradesh, India
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Lindström A, Pettersson F, Almqvist F, Berglund A, Kihlberg J, Linusson A. Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein−Ligand Complexes. J Chem Inf Model 2006; 46:1154-67. [PMID: 16711735 DOI: 10.1021/ci050323k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new approach is presented for predicting ligand binding to proteins using hierarchical partial-least-squares regression to latent structures (Hi-PLS). Models were based on information from the 2002 release of the PDBbind database containing (after in-house refinement) high-resolution X-ray crystallography and binding affinity (Kd or Ki) data for 612 protein-ligand complexes. The complexes were characterized by four different descriptor blocks: three-dimensional (3D) structural descriptors of the proteins, protein-ligand interactions according to the Validate scoring function, binding site surface areas, and ligand 2D and 3D descriptors. These descriptor blocks were used in Hi-PLS models, generated using both linear and nonlinear terms, to relate the characterizations to pKd/i. The results show that each of the four descriptor blocks contributed to the model, and the predictions of pKd/i of the internal test set gave a root-mean-square error of prediction (RMSEP) of 1.65. The data were further divided according to the structural classification of the proteins, and Hi-PLS models were constructed for the resulting subclasses. The models for the four subclasses differed considerably in terms of both their ability to predict pKd/i (with RMSEPs ranging from 0.8 to 1.56) and the descriptor block that had the strongest influence. The models were validated with an external test set of 174 complexes from the 2003 release of the PDBbind database. The overall results show that the presented Hi-PLS methodology could facilitate the difficult task of predicting binding affinity.
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Affiliation(s)
- Anton Lindström
- Organic Chemistry, Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
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Liao H, Aoyama C, Ishidate K, Teraoka H. Deletion and alanine mutation analyses for the formation of active homo- or hetero-dimer complexes of mouse choline kinase-α and -β. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1761:111-20. [PMID: 16490392 DOI: 10.1016/j.bbalip.2006.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 10/25/2022]
Abstract
Choline kinase (CK) is the first-step regulatory enzyme for the biosynthesis of phosphatidylcholine in all mammalian cells. It exists as at least three isoforms (alpha1, alpha2 and beta) that are encoded by two separate genes termed ck-alpha and ck-beta. The active enzyme has been proposed to consist of either their homo- or hetero-dimeric forms. Here, we report on the identification of several essential domains and amino acid residues involved in their active dimer formation. Full-length cDNAs or their truncated or alanine-mutated versions for mouse CK-alpha1 and CK-beta tagged with either HA or Myc at their N-termini were expressed in COS-7 cells. Each dimer formation was analyzed by immuno-precipitation followed by Western blotting. Kinetic analysis for CK reaction was performed with different expression products. Both the N-terminal domain-1 and C-terminal portions (E424-K430 for CK-alpha1 and Q379-K385 for CK-beta) were shown to be critical for the formation of active homo- or hetero-dimer complex. Interestingly, D320 in the CK-motif of CK-alpha1 was found to be essential for alpha1/alpha1 homo-dimerization but not for alpha1/beta hetero-dimerization. A mutation of the corresponding D276 of CK-beta to A276 did not show any effect on either its homo- or hetero-dimerization but it caused a strong inhibition of CK activity in either case.
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Affiliation(s)
- Huanan Liao
- Department of Pathological Biochemistry, Medical Research Institute, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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Scheeff ED, Bourne PE. Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol 2005; 1:e49. [PMID: 16244704 PMCID: PMC1261164 DOI: 10.1371/journal.pcbi.0010049] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 09/08/2005] [Indexed: 11/19/2022] Open
Abstract
The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase-like superfamily. The comparison of structures revealed a "universal core" domain consisting only of regions required for ATP binding and the phosphotransfer reaction. Remarkably, even within the universal core some kinase structures display notable changes, while still retaining essential activity. Hence, the protein kinase-like superfamily has undergone substantial structural and sequence revision over long evolutionary timescales. We constructed a phylogenetic tree for the superfamily using a novel approach that allowed for the combination of sequence and structure information into a unified quantitative analysis. When considered against the backdrop of species distribution and other metrics, our tree provides a compelling scenario for the development of the various kinase families from a shared common ancestor. We propose that most of the so-called "atypical kinases" are not intermittently derived from protein kinases, but rather diverged early in evolution to form a distinct phyletic group. Within the atypical kinases, the aminoglycoside and choline kinase families appear to share the closest relationship. These two families in turn appear to be the most closely related to the protein kinase family. In addition, our analysis suggests that the actin-fragmin kinase, an atypical protein kinase, is more closely related to the phosphoinositide-3 kinase family than to the protein kinase family. The two most divergent families, alpha-kinases and phosphatidylinositol phosphate kinases (PIPKs), appear to have distinct evolutionary histories. While the PIPKs probably have an evolutionary relationship with the rest of the kinase superfamily, the relationship appears to be very distant (and perhaps indirect). Conversely, the alpha-kinases appear to be an exception to the scenario of early divergence for the atypical kinases: they apparently arose relatively recently in eukaryotes. We present possible scenarios for the derivation of the alpha-kinases from an extant kinase fold.
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Affiliation(s)
- Eric D Scheeff
- San Diego Supercomputer Center, University of California, San Diego, California, United States of America.
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Kannan N, Neuwald AF. Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J Mol Biol 2005; 351:956-72. [PMID: 16051269 DOI: 10.1016/j.jmb.2005.06.057] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Revised: 06/21/2005] [Accepted: 06/23/2005] [Indexed: 10/25/2022]
Abstract
Statistical analysis of the functional constraints acting on eukaryotic protein kinases (EPKs) and on distantly related kinases suggests that EPK regulatory mechanisms evolved around an ancient structural component whose most distinctive features include the HxD-motif adjoining the catalytic loop, the F-helix, an F-helix aspartate, and the DFG-motif adjoined to the activation loop. The HxD-histidine constitutes a convergence point for signal integration, as conserved interactions link it to key catalytic residues, to the F-helix aspartate, and to both ends of the DFG-motif. These and other conserved features appear to be associated with DFG conformational changes and with coordinated movements possibly associated with phosphate transfer and ADP release. The EPKs have acquired structural features that link this core component to likely substrate-interacting regions at either end of the F-helix (most notably involving an F-helix tryptophan) and to three regions undergoing conformational changes upon kinase activation: the activation segment, the C-helix, and the nucleotide-binding pocket.
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Affiliation(s)
- Natarajan Kannan
- Cold Spring Harbor Laboratory, 1 Bungtown Road, P.O. Box 100, Cold Spring Harbor, NY 11724, USA
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Choi MG, Kurnov V, Kersting MC, Sreenivas A, Carman GM. Phosphorylation of the yeast choline kinase by protein kinase C. Identification of Ser25 and Ser30 as major sites of phosphorylation. J Biol Chem 2005; 280:26105-12. [PMID: 15919656 PMCID: PMC1383591 DOI: 10.1074/jbc.m503551200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Saccharomyces cerevisiae CKI1-encoded choline kinase catalyzes the committed step in phosphatidylcholine synthesis via the Kennedy pathway. The enzyme is phosphorylated on multiple serine residues, and some of this phosphorylation is mediated by protein kinase A. In this work we examined the hypothesis that choline kinase is also phosphorylated by protein kinase C. Using choline kinase as a substrate, protein kinase C activity was dose- and time-dependent and dependent on the concentrations of choline kinase (K(m) = 27 microg/ml) and ATP (K(m) = 15 microM). This phosphorylation, which occurred on a serine residue, was accompanied by a 1.6-fold stimulation of choline kinase activity. The synthetic peptide SRSSSQRRHS (V5max/K(m) = 17.5 mm(-1) micromol min(-1) mg(-1)) that contains the protein kinase C motif for Ser25 was a substrate for protein kinase C. A Ser25 to Ala (S25A) mutation in choline kinase resulted in a 60% decrease in protein kinase C phosphorylation of the enzyme. Phosphopeptide mapping analysis of the S25A mutant enzyme confirmed that Ser25 was a protein kinase C target site. In vivo the S25A mutation correlated with a decrease (55%) in phosphatidylcholine synthesis via the Kennedy pathway, whereas an S25D phosphorylation site mimic correlated with an increase (44%) in phosphatidylcholine synthesis. Although the S25A (protein kinase C site) mutation did not affect the phosphorylation of choline kinase by protein kinase A, the S30A (protein kinase A site) mutation caused a 46% reduction in enzyme phosphorylation by protein kinase C. A choline kinase synthetic peptide (SQRRHSLTRQ) containing Ser30 was a substrate (V(max)/K(m) = 3.0 mm(-1) micromol min(-1) mg(-1)) for protein kinase C. Comparison of phosphopeptide maps of the wild type and S30A mutant choline kinase enzymes phosphorylated by protein kinase C confirmed that Ser30 was also a target site for protein kinase C.
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Affiliation(s)
| | | | | | | | - George M. Carman
- #To whom correspondence and reprint requests should be addressed. Dept. of Food Science, Rutgers University, 65 Dudley Rd., New Brunswick, NJ 08901. Tel: 732-932-9611 (ext. 217); E-mail:
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Cheek S, Ginalski K, Zhang H, Grishin NV. A comprehensive update of the sequence and structure classification of kinases. BMC STRUCTURAL BIOLOGY 2005; 5:6. [PMID: 15771780 PMCID: PMC1079889 DOI: 10.1186/1472-6807-5-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 03/16/2005] [Indexed: 12/02/2022]
Abstract
Background A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years. However, the framework of the original two-tier classification scheme (in families and fold groups) remains sufficient to describe all available kinases. Overall, the kinase sequences were classified into 25 families of homologous proteins, wherein 22 families (~98.8% of all sequences) for which three-dimensional structures are known fall into 10 fold groups. These fold groups not only include some of the most widely spread proteins folds, such as the Rossmann-like fold, ferredoxin-like fold, TIM-barrel fold, and antiparallel β-barrel fold, but also all major classes (all α, all β, α+β, α/β) of protein structures. Fold predictions are made for remaining kinase families without a close homolog with solved structure. We also highlight two novel kinase structural folds, riboflavin kinase and dihydroxyacetone kinase, which have recently been characterized. Two protein families previously annotated as kinases are removed from the classification based on new experimental data. Conclusion Structural annotations of all kinase families are now revealed, including fold descriptions for all globular kinases, making this the first large functional class of proteins with a comprehensive structural annotation. Potential uses for this classification include deduction of protein function, structural fold, or enzymatic mechanism of poorly studied or newly discovered kinases based on proteins in the same family.
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Affiliation(s)
- Sara Cheek
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Krzysztof Ginalski
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Bioinformatics Laboratory, Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Hong Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
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