Sandbox 201: Difference between revisions

Line 55:

:Metal ions are essential for the nucleotidyltransferase catalysis by all T4 DNA and T4 RNA ligases, which use the same two-metal ions mechanism.

:The enzyme binds <scene name='Sandbox_201/Mg/1'>two Mg2+ ions.</scene> The true substrate in the adenylation reaction is the ATP-Mg2+ complex <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref>, but nucleotidyltransferase enzymes cannot bind ATP-Mg2 directly. They bind ATP-Mg first, then a second Mg2+ ion. A Mg2+ ion interacts ~~also~~ with one phosphoryl oxygen in AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain.

:The enzyme binds <scene name='Sandbox_201/Mg/1'>two Mg2+ ions.</scene> The true substrate in the adenylation reaction is the ATP-Mg2+ complex <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref>, but nucleotidyltransferase enzymes cannot bind ATP-Mg2 directly. They bind ATP-Mg first, then a second Mg2+ ion. <scene name='Sandbox_201/Mg_apc_residues/1'>A Mg2+ ion interacts via hydrogen bonds</scene> with one phosphoryl oxygen from AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain.

:The enzyme binds four Ca2+ ions. Two are coordinated to six water molecules. :They do not directly interact with the enzyme, but via water molecules interacting with Glu227, Glu159, Lys99, Glu100, and Tyr246. They also interact with one phosphoryl oxygen of the AMPcPP. Two other are coordinated to six water molecules and interact with three enzyme residues (Asp212 in chain A and Ile211 and Asp212 in chain B).

@@ Line 55: / Line 55: @@
 :Metal ions are essential for the nucleotidyltransferase catalysis by all T4 DNA and T4 RNA ligases, which use the same two-metal ions mechanism.
-:The enzyme binds <scene name='Sandbox_201/Mg/1'>two Mg<sup>2+</sup> ions.</scene> The true substrate in the adenylation reaction is the ATP-Mg<sup>2+</sup> complex <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref>, but nucleotidyltransferase enzymes cannot bind ATP-Mg<sub>2</sub> directly. They bind ATP-Mg first, then a second Mg<sup>2+</sup> ion. A Mg<sup>2+</sup> ion interacts also with one phosphoryl oxygen in AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain.
+:The enzyme binds <scene name='Sandbox_201/Mg/1'>two Mg<sup>2+</sup> ions.</scene> The true substrate in the adenylation reaction is the ATP-Mg<sup>2+</sup> complex <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref>, but nucleotidyltransferase enzymes cannot bind ATP-Mg<sub>2</sub> directly. They bind ATP-Mg first, then a second Mg<sup>2+</sup> ion. <scene name='Sandbox_201/Mg_apc_residues/1'>A Mg<sup>2+</sup> ion interacts via hydrogen bonds</scene> with one phosphoryl oxygen from AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain.
 :The enzyme binds four Ca<sup>2+</sup> ions. Two are coordinated to six water molecules. :They do not directly interact with the enzyme, but via water molecules interacting with Glu227, Glu159, Lys99, Glu100, and Tyr246. They also interact with one phosphoryl oxygen of the AMPcPP. Two other are coordinated to six water molecules and interact with three enzyme residues (Asp212 in chain A and Ile211 and Asp212 in chain B).

Sandbox 201: Difference between revisions

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