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Rivera-Pérez WA, Yépes-Pérez AF, Martínez-Pabón MC. Molecular docking and in silico studies of the physicochemical properties of potential inhibitors for the phosphotransferase system of Streptococcus mutans. Arch Oral Biol 2018; 98:164-175. [PMID: 30500666 DOI: 10.1016/j.archoralbio.2018.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 10/27/2022]
Abstract
This study identified potential inhibitory compounds of the phosphoenolpyruvate-sugar. Phosphotransferase system of S. mutans, specifically enzyme II mannose transporter (EIIMan) in its subunits IIA, IIB and IIC by means of a selection protocol and in silico molecular analysis. Intervening the phosphotransferase system would compromise the physiological behavior and the pathogenic expression of S. mutans, and possibly other acidogenic bacteria that use phosphotransferases in their metabolism-making the phosphotransferase system a therapeutic target for the selective control of acidogenic microorganisms in caries control. Several computational techniques were used to evaluate molecular, physicochemical, and toxicological aspects of various compounds. Molecular docking was used to calculate the binding potential (ΔG) between receptor protein subunits and more than 836,000 different chemical compounds from the ZINC database. Physicochemical parameters related to the compounds' pharmacokinetic and pharmacodynamic indicators were evaluated, including absorption, distribution, metabolism, excretion, and toxicity (ADMET), and chemical analysis characterized the compounds structures. Thirteen compounds with EII binding potential of the phosphotransferase system of S. mutans and favorable ADMET properties were identified. Six spirooxindoles and three pyrrolidones stand out from the found compounds; unique structural characteristics of spirooxindoles and pyrrolidones associated with various reported biological activities like anti-microbial, antiinflammatory, anticancer, nootropic, neuroprotective and antiepileptic effects, among other pharmacological effects with surprising differences in terms of mechanisms of action. Following studies will provide more evidence of the action of these compounds on the phosphotransferase system of S. mutans, and its possible applications.
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Affiliation(s)
- Wbeimar Andrey Rivera-Pérez
- Faculty of Dentistry, University of Antioquia- UdeA, 64 Street No. 52-59, Block 31, Oral Microbiology Laboratory No. 216, Health Area, Medellin, Colombia.
| | - Andrés Felipe Yépes-Pérez
- Exact and Natural Sciences School, University of Antioquia-UdeA, Universidad de Antioquia. 67 street No. 53-108, Block 2, Chemistry of Colombian, Plants Laboratory, Office 330, Medellin, Colombia.
| | - Maria Cecilia Martínez-Pabón
- Faculty of Dentistry, University of Antioquia- UdeA, 64 Street No. 52-59, Block 31, Oral Microbiology Laboratory No. 216, Health Area, Medellin, Colombia.
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Luo P, Dai S, Zeng J, Duan J, Shi H, Wang J. Inward-facing conformation of l-ascorbate transporter suggests an elevator mechanism. Cell Discov 2018; 4:35. [PMID: 30038796 PMCID: PMC6048161 DOI: 10.1038/s41421-018-0037-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
Various bacteria can ferment vitamin C (l-ascorbate) under anaerobic conditions via the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTSasc system is composed of two soluble energy-coupling proteins (EI and HPr) and an enzyme II complex (EIIA, EIIB, and EIIC) for the anaerobic uptake of ascorbate and its phosphorylation to l-ascorbate 6-phosphate in vivo. Crystal structures of the ascorbate-bound EIIC component from Escherichia coli are available in outward-open and occluded conformations, suggesting a possible elevator mechanism of membrane transport. Despite these advances, it remains unclear how EIIC actually transports the substrate across the membrane and interacts with EIIB, which transfers its phosphate group to the EIIC-embedding ascorbate. Here, we present the crystal structure of the EIICasc component from Pasteurella multocida in the inward-facing conformation. By comparing three conformational states, we confirmed the original proposed model: the ascorbate translocation can be achieved by a rigid-body movement of the substrate-binding core domain relative to the V motif domain, which brings along the transmembrane helices TM2 and TM7 of the V motif domain to undergo a winding at the pivotal positions. Together with an in vivo transport assay, we completed the picture of the transport cycle of the ascorbate superfamily of membrane-spanning EIIC components of the PTS system.
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Affiliation(s)
- Ping Luo
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Shuliu Dai
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jianwei Zeng
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Hui Shi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
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Park J, Kim MS, Joo K, Jhon GJ, Berry EA, Lee J, Shin DH. Crystal Structure of Hypothetical Fructose-Specific EIIB from Escherichia coli. Mol Cells 2016; 39:495-500. [PMID: 27215198 PMCID: PMC4916401 DOI: 10.14348/molcells.2016.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 11/27/2022] Open
Abstract
We have solved the crystal structure of a predicted fructose-specific enzyme IIB(fruc) from Escherichia coli (EcEIIB(fruc)) involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system transferring carbohydrates across the cytoplasmic membrane. EcEIIB(fruc) belongs to a sequence family with more than 5,000 sequence homologues with 25-99% amino-acid sequence identity. It reveals a conventional Rossmann-like α-β-α sandwich fold with a unique β-sheet topology. Its C-terminus is longer than its closest relatives and forms an additional β-strand whereas the shorter C-terminus is random coil in the relatives. Interestingly, its core structure is similar to that of enzyme IIB(cellobiose) from E. coli (EcIIB(cel)) transferring a phosphate moiety. In the active site of the closest EcEIIB(fruc) homologues, a unique motif CXXGXAHT comprising a P-loop like architecture including a histidine residue is found. The conserved cysteine on this loop may be deprotonated to act as a nucleophile similar to that of EcIIB(cel). The conserved histidine residue is presumed to bind the negatively charged phosphate. Therefore, we propose that the catalytic mechanism of EcEIIB(fruc) is similar to that of EcIIB(cel) transferring phosphoryl moiety to a specific carbohydrate.
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Affiliation(s)
- Jimin Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha Womans University, Seoul 03760,
Korea
| | - Mi-Sun Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha Womans University, Seoul 03760,
Korea
| | - Keehyung Joo
- Center for insilico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455,
Korea
| | - Gil-Ja Jhon
- Department of Chemistry and Nano Science, Global Top5 Research Program, Ewha Womans University, Seoul 03760,
Korea
| | - Edward A. Berry
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York,
USA
| | - Jooyoung Lee
- Center for insilico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455,
Korea
| | - Dong Hae Shin
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha Womans University, Seoul 03760,
Korea
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Wu X, Hou J, Chen X, Chen X, Zhao W. Identification and functional analysis of the L-ascorbate-specific enzyme II complex of the phosphotransferase system in Streptococcus mutans. BMC Microbiol 2016; 16:51. [PMID: 27001419 PMCID: PMC4802650 DOI: 10.1186/s12866-016-0668-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/07/2016] [Indexed: 12/27/2022] Open
Abstract
Background Streptococcus mutans is the primary etiological agent of human dental caries. It can metabolize a wide variety of carbohydrates and produce large amounts of organic acids that cause enamel demineralization. Phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) plays an important role in carbohydrates uptake of S. mutans. The ptxA and ptxB genes in S. mutans encode putative enzyme IIA and enzyme IIB of the L-ascorbate-specific PTS. The aim of this study was to analyze the function of these proteins and understand the transcriptional regulatory mechanism. Results ptxA−, ptxB−, as well as ptxA−, ptxB− double-deletion mutants all had more extended lag phase and lower growth yield than wild-type strain UA159 when grown in the medium using L-ascorbate as the sole carbon source. Acid production and acid killing assays showed that the absence of the ptxA and ptxB genes resulted in a reduction in the capacity for acidogenesis, and all three mutant strains did not survive an acid shock. According to biofilm and extracellular polysaccharides (EPS) formation analysis, all the mutant strains formed much less prolific biofilms with small amounts of EPS than wild-type UA159 when using L-ascorbate as the sole carbon source. Moreover, PCR analysis and quantitative real-time PCR revealed that sgaT, ptxA, ptxB, SMU.273, SMU.274 and SMU.275 appear to be parts of the same operon. The transcription levels of these genes were all elevated in the presence of L-ascorbate, and the expression of ptxA gene decreased significantly once ptxB gene was knockout. Conclusions The ptxA and ptxB genes are involved in the growth, aciduricity, acidogenesis, and formation of biofilms and EPS of S. mutans when L-ascorbate is the sole carbon source. In addition, the expression of ptxA is regulated by ptxB. ptxA, ptxB, and the upstream gene sgaT, the downstream genes SMU.273, SMU.274 and SMU.275 appear to be parts of the same operon, and L-ascorbate is a potential inducer of the operon. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0668-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyu Wu
- Department of Stomatology, Nanfang Hospital and College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Jin Hou
- Department of Stomatology, Nanfang Hospital and College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaodan Chen
- Department of Stomatology, the Second Affiliated Hospital of Shantou University, Shantou, Guangdong, China
| | - Xuan Chen
- Department of Stomatology, Nanfang Hospital and College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Wanghong Zhao
- Department of Stomatology, Nanfang Hospital and College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China.
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Hammerstrom TG, Horton LB, Swick MC, Joachimiak A, Osipiuk J, Koehler TM. Crystal structure of Bacillus anthracis virulence regulator AtxA and effects of phosphorylated histidines on multimerization and activity. Mol Microbiol 2014; 95:426-41. [PMID: 25402841 DOI: 10.1111/mmi.12867] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2014] [Indexed: 12/22/2022]
Abstract
The Bacillus anthracis virulence regulator AtxA controls transcription of the anthrax toxin genes and capsule biosynthetic operon. AtxA activity is elevated during growth in media containing glucose and CO(2)/bicarbonate, and there is a positive correlation between the CO(2)/bicarbonate signal, AtxA activity and homomultimerization. AtxA activity is also affected by phosphorylation at specific histidines. We show that AtxA crystallizes as a dimer. Distinct folds associated with predicted DNA-binding domains (HTH1 and HTH2) and phosphoenolpyruvate: carbohydrate phosphotransferase system-regulated domains (PRD1 and PRD2) are apparent. We tested AtxA variants containing single and double phosphomimetic (His→Asp) and phosphoablative (His→Ala) amino acid changes for activity in B. anthracis cultures and for protein-protein interactions in cell lysates. Reduced activity of AtxA H199A, lack of multimerization and activity of AtxAH379D variants, and predicted structural changes associated with phosphorylation support a model for control of AtxA function. We propose that (i) in the AtxA dimer, phosphorylation of H199 in PRD1 affects HTH2 positioning, influencing DNA-binding; and (ii) phosphorylation of H379 in PRD2 disrupts dimer formation. The AtxA structure is the first reported high-resolution full-length structure of a PRD-containing regulator, and can serve as a model for proteins of this family, especially those that link virulence to bacterial metabolism.
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Affiliation(s)
- Troy G Hammerstrom
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Li L, Nan J, Li D, Brostromer E, Wang Z, Liu C, Hou Q, Fan X, Ye Z, Su XD. Structural genomics studies of human caries pathogen Streptococcus mutans. ACTA ACUST UNITED AC 2014; 15:91-9. [PMID: 24474570 DOI: 10.1007/s10969-014-9172-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/17/2014] [Indexed: 10/25/2022]
Abstract
Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.
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Affiliation(s)
- Lanfen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China,
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Reinelt S, Koch B, Hothorn M, Hengstenberg W, Welti S, Scheffzek K. Structure of the Enterococcus faecalis EIIA(gnt) PTS component. Biochem Biophys Res Commun 2009; 388:626-9. [PMID: 19682976 DOI: 10.1016/j.bbrc.2009.08.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 08/07/2009] [Indexed: 11/29/2022]
Abstract
In Eubacteria, the utilization of a number of extracellular carbohydrates is mediated by sugar specific phosphoenolepyruvate (PEP) dependent sugar phosphotransferase systems (PTSs), which simultaneously import und phosphorylate their target sugars. Here, we report the crystal structure of the EIIA(gnt) component of the so far little investigated Enterococcus faecalis gluconate specific PTS. The crystal structure shows a tightly interacting dimer of EIIA(gnt) which is structurally similar to the related EIIA(man) from Escherichia coli. Homology modeling of E. faecalis HPr, EIIB(man) and their complexes with EIIA(man) suggests that despite moderate sequence identity between EIIA(man) and EIIA(gnt), the active sites closely match the situation observed in the E. coli system with His-9 of EIIA(gnt) being the likely phosphoryl group carrier. We therefore propose that the phosphoryl transfer reactions involving EIIA(gnt) proceed according to a mechanism analog to the one described for E. coli EIIA(man).
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Affiliation(s)
- Stefan Reinelt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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