Sandbox Reserved 702: Difference between revisions
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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='500' frame='true' align='right' caption=' | <Structure load='1lvc' size='500' frame='true' align='right' caption='Magnesium ions coordinated by D491, D498 and H577.' /> | ||
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==Mechanism of adenylyl cyclase of edema factor== | ==Mechanism of adenylyl cyclase of edema factor== | ||
<Structure load='1lvc' size='500' frame='true' align='right' caption='Amino acids which play a key role in the adenylyl cyclase reaction.' /> | |||
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 interactss with it to restrict the rotation of the ribose. 3'OH is so hold in place for its nucleophilic attack durung the catalysis. Moreover, theprotonated histidine 351 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 [[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 interactss with it to restrict the rotation of the ribose. 3'OH is so hold in place for its nucleophilic attack durung the catalysis. Moreover, theprotonated histidine 351 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/ | 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, histidine 351 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: arginine 329, lysine 353, lysine 372 and lysine 346. <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: arginine 329, lysine 353, lysine 372 and lysine 346. <ref> PMID: 15719022</ref> | ||
