Sandbox Reserved 702: Difference between revisions
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*cyclic nucleotide gated channels | *cyclic nucleotide gated channels | ||
*guanine nucleotide exchange factor for Ras GTPase homologs Rap1 and Rap2. <ref>Fouet, A. 2009. The surface of Bacillus anthracis. Mol. Aspects Med. 30:374–385</ref> <ref>Moayeri, M., and S. H. Leppla. 2009. Cellular and systemic effects of anthrax lethal toxin and edema toxin. Mol. Aspects Med. 30:439–455</ref> | *guanine nucleotide exchange factor for Ras GTPase homologs Rap1 and Rap2. <ref>Fouet, A. 2009. The surface of Bacillus anthracis. Mol. Aspects Med. 30:374–385</ref> <ref>Moayeri, M., and S. H. Leppla. 2009. Cellular and systemic effects of anthrax lethal toxin and edema toxin. Mol. Aspects Med. 30:439–455</ref> | ||
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*'''Lethal factor (LF)''' | *'''Lethal factor (LF)''' | ||
LF is a zinc-mediated metalloprotease that cleaves mitogen-activated protein kinase kinases (MEKs). This impairs cell signaling, and results in the induction of apoptosis. <ref>Klimpel, K. R., N. Arora, and S. H. Leppla. 1994. Anthrax toxin lethal factor contains a zinc metalloprotease consensus sequence which is required for lethal toxin activity. Mol. Microbiol. 13:1093–1100</ref> | LF is a zinc-mediated metalloprotease that cleaves mitogen-activated protein kinase kinases (MEKs). This impairs cell signaling, and results in the induction of apoptosis. <ref>Klimpel, K. R., N. Arora, and S. H. Leppla. 1994. Anthrax toxin lethal factor contains a zinc metalloprotease consensus sequence which is required for lethal toxin activity. Mol. Microbiol. 13:1093–1100</ref> | ||
*'''Edema factor (EF)''' | *'''Edema factor (EF)''' | ||
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===Molecular basis for the activation of edema factor by calmodulin=== | ===Molecular basis for the activation of edema factor by calmodulin=== | ||
<Structure load='1k8t' size='300' frame='true' align='left' /> | |||
<scene name='Sandbox_Reserved_702/1k8t/2'>Structural basis for </scene> the activation of anthrax adenylyl cyclase by calmodulin. (PDB 1k8t)<ref>http://www.rcsb.org/pdb/explore/explore.do?structureId=1k8t</ref> | |||
Legend: {{Template:ColorKey Composition Protein}} | |||
{{Template:ColorKey Composition Ligand}} | |||
{{Template:ColorKey Composition Solvent}} | |||
The '''helical domain of the edema factor''' interacts with the [[adenylate cyclase]] domain and '''switch C''' in the '''absence of [[calmodulin]]'''. This locks the enzyme in an '''inactive''' state. | The '''helical domain of the edema factor''' interacts with the [[adenylate cyclase]] domain and '''switch C''' in the '''absence of [[calmodulin]]'''. This locks the enzyme in an '''inactive''' state. | ||
The '''binding of [[calmodulin]]''' on four discrete regions dicrupts most of those interaction allowing the enzyme to switch in an '''active''' form. This takes place in two steps. <ref> PMID: 19560485</ref> | The '''binding of [[calmodulin]]''' on four discrete regions dicrupts most of those interaction allowing the enzyme to switch in an '''active''' form. This takes place in two steps. <ref> PMID: 19560485</ref> | ||
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==Two magnesium ions are coordinated by the catalytic site== | ==Two magnesium ions are coordinated by the catalytic site== | ||
<Structure load='1lvc' size=' | <Structure load='1lvc' size='400' frame='true' align='right' caption='Magnesium ions coordinated by D491, D498 and H577.' /> | ||
[[Adenylyl cyclase]] activity of the edema factor requires two magnesium ions. One of them is coordinated by <scene name='Sandbox_Reserved_702/Asp_and_his/2'>two aspartic residues (D491 and D493) and the histidine 577.</scene> | [[Adenylyl cyclase]] activity of the edema factor requires two magnesium ions. One of them is coordinated by <scene name='Sandbox_Reserved_702/Asp_and_his/2'>two aspartic residues (D491 and D493) and the histidine 577.</scene> | ||
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<scene name='Sandbox_Reserved_702/Histidine_351/1'>Histidine 351</scene> also plays a key role in the [[adenylyl cyclase]] reaction. Histidine is a crucial amino acid because its pKa (6.8) is close to pH of cytoplasm. | <scene name='Sandbox_Reserved_702/Histidine_351/1'>Histidine 351</scene> also plays a key role in the [[adenylyl cyclase]] reaction. Histidine is a crucial amino acid because its pKa (6.8) is close to pH of cytoplasm. | ||
It may intervene in proton-transfer reactions. Histidine 351 has a critical role in the catalytic activity of edema factor but is not a catalytic base. Since it is about 6.0 Å away from the 3'O of cAMP, its role is to allow a water molecule to enter between them. Histidine does not act as a general base (acceptor of 3'OH proton), but is facilitates an increase in the concentration of HO- ions in the proximity of the 3'OH group. <ref> PMID: 15719022</ref> | It may intervene in proton-transfer reactions. Histidine 351 has a critical role in the catalytic activity of edema factor but is not a catalytic base. Since it is about 6.0 Å away from the 3'O of cAMP, its role is to allow a water molecule to enter between them. Histidine does not act as a general base (acceptor of 3'OH proton), but is facilitates an increase in the concentration of HO- ions in the proximity of the 3'OH group. <ref> PMID: 15719022</ref> | ||
==Mechanism of adenylyl cyclase of edema factor== | ==Mechanism of adenylyl cyclase of edema factor== | ||
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The current model for the catalytic reaction of edema factor is the following: the reaction is mediated by the '''nucleophilic attack''' of the 3' oxygen atom on the α-phosphate. Indeed, this oxygen in near the α-phosphate. The distance between the nucleophile 3'O and the α-phosphate atom os ATP is shorter than 3.5 Å. A 3'-endo conformation of the ribose and a direct coordination of the 3'O atom by the catalytic magnesium ion is the ideal geometry for the initiation of the nucleophilic attack of the 3'O on the α-phosphate. <ref> PMID: 15719022</ref> | The current model for the catalytic reaction of edema factor is the following: the reaction is mediated by the '''nucleophilic attack''' of the 3' oxygen atom on the α-phosphate. Indeed, this oxygen in near the α-phosphate. The distance between the nucleophile 3'O and the α-phosphate atom os ATP is shorter than 3.5 Å. A 3'-endo conformation of the ribose and a direct coordination of the 3'O atom by the catalytic magnesium ion is the ideal geometry for the initiation of the nucleophilic attack of the 3'O on the α-phosphate. <ref> PMID: 15719022</ref> | ||
The [[adenylyl cyclase]] reaction takes place in several steps: '''binding of ATP''' to the edema factor, enabling the '''deprotonation''' of 3'OH, '''stabilization''' of the penta-coordinated phosphorus intermediate and finally the '''release of cAMP''' and pyrophosphate. The enzyme binds its substrate, ATP and asparagine 583 interacts with it to restrict the rotation of the ribose. 3'OH is so hold in place for its nucleophilic attack during the catalysis. Moreover, the protonated <scene name='Sandbox_Reserved_702/ | The [[adenylyl cyclase]] reaction takes place in several steps: '''binding of ATP''' to the edema factor, enabling the '''deprotonation''' of 3'OH, '''stabilization''' of the penta-coordinated phosphorus intermediate and finally the '''release of cAMP''' and pyrophosphate. The enzyme binds its substrate, ATP and asparagine 583 interacts with it to restrict the rotation of the ribose. 3'OH is so hold in place for its nucleophilic attack during the catalysis. Moreover, the protonated <scene name='Sandbox_Reserved_702/Histidine_351/1'>histidine 351</scene> stabilizes the HO- ion near the 3'OH group. Another model is that a neutral histidine deprotonates a water molecule and that the resulting HO- ion facilitates the deprotonation of 3'OH of ATP. <ref> PMID: 15719022</ref> | ||
The '''magnesium ion''' that is coordinated by <scene name='Sandbox_Reserved_702/Asp_and_his/2'>aspartates 491 and 493 and histidine 577</scene> is localized near the 3'OH of ATP. Since it is positively charged, it stabilizes the negative charge of the 3'-oxyanion and thus facilitates the deprotonation of 3'OH. The action of this ion and of <scene name='Sandbox_Reserved_702/ | The '''magnesium ion''' that is coordinated by <scene name='Sandbox_Reserved_702/Asp_and_his/2'>aspartates 491 and 493 and histidine 577</scene> is localized near the 3'OH of ATP. Since it is positively charged, it stabilizes the negative charge of the 3'-oxyanion and thus facilitates the deprotonation of 3'OH. The action of this ion and of <scene name='Sandbox_Reserved_702/Histidine_351/1'>histidine 351</scene> can be additive. To summarise, <scene name='Sandbox_Reserved_702/Histidine_351/1'>histidine 351</scene> increases the local pH by attracting HO-, and the metal ion decreases the pKa of the 3'OH group. Maybe the magnesium ion also stabilizes the reaction intermediate by moving towards the non-bridging oxygen of α-phosphate durung the nucleophilic attack. <ref> PMID: 15719022</ref> | ||
The '''second magnesium ion''', that is coordinated with the oxygens of the phosphates of ATP, facilitates the bond breakage between α and β-phosphates. Indeed, it stabilizes the resulting negative charges. The stabilisation of the negative charged intermediate is also performed by different positive charged residues: <scene name='Sandbox_Reserved_702/Positive_charged_residues/1'>arginine 329, lysine 353, lysine 372 and lysine 346.</scene> <ref> PMID: 15719022</ref> | The '''second magnesium ion''', that is coordinated with the oxygens of the phosphates of ATP, facilitates the bond breakage between α and β-phosphates. Indeed, it stabilizes the resulting negative charges. The stabilisation of the negative charged intermediate is also performed by different positive charged residues: <scene name='Sandbox_Reserved_702/Positive_charged_residues/1'>arginine 329, lysine 353, lysine 372 and lysine 346.</scene> <ref> PMID: 15719022</ref> | ||
The products, pysophosphate and cyclic AMP dissociate through different solvent accessible channels in a two-step process facilitated by product protonation. They are linked to the enzyme by electrostatic interactions with the magnesium ions. The binding of a water molecule to the ions is competitive with thier binding to reaction products and breaks the electrostatic links. Ligands are progressively solvated. In a first time the most important electrostatic interactions are preserved. This depends on the flexibility of the active site. Then the electrostatic interactions are broken and the products can diffuse into solvent. <ref> PMID: 21425348</ref> | The products, pysophosphate and cyclic AMP dissociate through different solvent accessible channels in a two-step process facilitated by product protonation. They are linked to the enzyme by electrostatic interactions with the magnesium ions. The binding of a water molecule to the ions is competitive with thier binding to reaction products and breaks the electrostatic links. Ligands are progressively solvated. In a first time the most important electrostatic interactions are preserved. This depends on the flexibility of the active site. Then the electrostatic interactions are broken and the products can diffuse into solvent. <ref> PMID: 21425348</ref> | ||
==Prevention and treatment== | ==Prevention and treatment== | ||
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===Structural comparison of AC families and the development of selective EF inhibitor=== | ===Structural comparison of AC families and the development of selective EF inhibitor=== | ||
There are at least six classes of [[adenylyl cyclase]] (the classification is based on their primary sequence). Five classes are found only in bacteria and the last one, class III, exists as well in prokaryotes as in eukaryotes. Class II [[adenylyl cyclase]] are secreted by pathogenic bacteria and the edema factor belongs to this class. The catalytic site of these several classes are different. This enables the fact that some molecules could '''inhibit the adenylyl cyclase toxins without inhibiting those of the class III'''. Inhibitors can be designed to interfere either with the binding of [[calmodulin]] or with the binding of the substrate. | There are at least six classes of [[adenylyl cyclase]] (the classification is based on their primary sequence). Five classes are found only in bacteria and the last one, class III, exists as well in prokaryotes as in eukaryotes. Class II [[adenylyl cyclase]] are secreted by pathogenic bacteria and the edema factor belongs to this class. The catalytic site of these several classes are different. This enables the fact that some molecules could '''inhibit the adenylyl cyclase toxins without inhibiting those of the class III'''. Inhibitors can be designed to interfere either with the binding of [[calmodulin]] or with the binding of the substrate. <ref>Shen et al. 2004</ref> | ||
These inhibitors could be further developed as an anti-anthrax treatment, which will be administered with antibiotics. Among those, the most potent EF inhibitor is an approved drug, '''Adefovir'''. Adefovir can selectively '''inhibit the activity of EF''' | These inhibitors could be further developed as an anti-anthrax treatment, which will be administered with antibiotics. Among those, the most potent EF inhibitor is an approved drug, '''Adefovir'''. Adefovir can selectively '''inhibit the activity of EF''' with no inhibition of the activity of endogenous host AC. | ||
Adefovir is an acyclic nucleoside and it can treat chronic hepatitis B virus infection. '''Tenofovir''', another acyclic nucleoside which is a drug against '''human immunodeficiency virus''', also show high affinity to EF. <ref>Suryanarayana et al., Distinct Interactions of 2′- and 3′-O-(N-Methyl)anthraniloyl-Isomers of ATP and GTP with the Adenylyl Cyclase Toxin of Bacillus anthracis, Edema Factor, Biochem Pharmacol. 2009 August 1; 78(3): 224–230</ref> | Adefovir is an acyclic nucleoside and it can treat chronic hepatitis B virus infection. '''Tenofovir''', another acyclic nucleoside which is a drug against '''human immunodeficiency virus''', also show high affinity to EF. <ref>Suryanarayana et al., Distinct Interactions of 2′- and 3′-O-(N-Methyl)anthraniloyl-Isomers of ATP and GTP with the Adenylyl Cyclase Toxin of Bacillus anthracis, Edema Factor, Biochem Pharmacol. 2009 August 1; 78(3): 224–230</ref> | ||
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[[Category: Protein-protein complex]] | [[Category: Protein-protein complex]] | ||
=Contributors= | =Proteopedia Page Contributors and Editors= | ||
Charlotte Kern - Aude Zimmermann ESBS | Charlotte Kern - Aude Zimmermann ESBS | ||
