1e22: Difference between revisions

Revision as of 13:22, 21 February 2008

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP

OverviewOverview

Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid carboxylate group and the tRNA acceptor stem is supplied by coupling the reaction to the hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to the family of class II synthetases and carries out a two-step reaction, in which lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. Crystals of the thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1 A resolution have been used to determine crystal structures of the enzyme in the presence of lysine, the lysyl-adenylate intermediate, and the nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained from crystals soaked in a solution containing ATP and Mn(2+). The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilize the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding.

About this StructureAbout this Structure

1E22 is a Single protein structure of sequence from Escherichia coli with , , and as ligands. Active as Lysine--tRNA ligase, with EC number 6.1.1.6 Full crystallographic information is available from OCA.

ReferenceReference

Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction., Desogus G, Todone F, Brick P, Onesti S, Biochemistry. 2000 Jul 25;39(29):8418-25. PMID:10913247

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-[[Image:1e22.gif|left|200px]]<br /><applet load="1e22" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1e22.gif|left|200px]]<br /><applet load="1e22" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1e22, resolution 2.43&Aring;" />
 '''LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP'''<br />
 ==Overview==
-Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by, catalyzing the specific aminoacylation of tRNA. The energy required for, the formation of the ester bond between the amino acid carboxylate group, and the tRNA acceptor stem is supplied by coupling the reaction to the, hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to, the family of class II synthetases and carries out a two-step reaction, in, which lysine is activated by being attached to the alpha-phosphate of AMP, before being transferred to the cognate tRNA. Crystals of the, thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1, A resolution have been used to determine crystal structures of the enzyme, in the presence of lysine, the lysyl-adenylate intermediate, and the, nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained, from crystals soaked in a solution containing ATP and Mn(2+). The refined, crystal structures give "snapshots" of the active site corresponding to, key steps in the aminoacylation reaction and provide the structural, framework for understanding the mechanism of lysine activation. The active, site of LysU is shaped to position the substrates for the nucleophilic, attack of the lysine carboxylate on the ATP alpha-phosphate. No residues, are directly involved in catalysis, but a number of highly conserved amino, acids and three metal ions coordinate the substrates and stabilize the, pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine, binding.
+Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid carboxylate group and the tRNA acceptor stem is supplied by coupling the reaction to the hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to the family of class II synthetases and carries out a two-step reaction, in which lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. Crystals of the thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1 A resolution have been used to determine crystal structures of the enzyme in the presence of lysine, the lysyl-adenylate intermediate, and the nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained from crystals soaked in a solution containing ATP and Mn(2+). The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilize the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding.
 ==About this Structure==
-E22 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, LYS, ACP and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysine--tRNA_ligase Lysine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.6 6.1.1.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1E22 OCA].
+E22 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=LYS:'>LYS</scene>, <scene name='pdbligand=ACP:'>ACP</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysine--tRNA_ligase Lysine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.6 6.1.1.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E22 OCA].
 ==Reference==
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 [[Category: protein biosynthesis]]
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