1jjc: Difference between revisions

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Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese

OverviewOverview

The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution. Crystals of native PheRS were soaked in a solution containing phenylalanine and ATP in the presence of Mn(2+) ions. The first step of the aminoacylation reaction proceeds within the crystals, resulting in Phe-AMP formation at the active site. Specific recognition of the phenylalanine portion of the Phe-AMP is achieved by interactions of the phenyl ring of Phe-AMP with two neighbouring residues, Phealpha258 and Phealpha260. No manganese ions were observed within the active site; their role in the formation of the transition state may be assigned to a number of polar residues and water molecules. In the anomalous Fourier difference map, a divalent metal ion was detected at the interface of the alpha- and beta-subunits at a short distance from motif 3 residues participating in the substrate binding. A sulfate ion, which was identified on the protein surface, may mediate the interactions of PheRS with DNA. Visible conformational changes were detected in the active-site area adjacent to the position of the Phe-AMP, compared with the structure of PheRS complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate). Based on the known structures of the substrate-free enzyme and its complexes with various ligands, a general scheme for the phenylalanylation mechanism is proposed.

About this StructureAbout this Structure

1JJC is a Protein complex structure of sequences from Thermus thermophilus with , and as ligands. Active as Phenylalanine--tRNA ligase, with EC number 6.1.1.20 Full crystallographic information is available from OCA.

ReferenceReference

Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese., Fishman R, Ankilova V, Moor N, Safro M, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1534-44. Epub 2001, Oct 25. PMID:11679717

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-[[Image:1jjc.gif|left|200px]]<br /><applet load="1jjc" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1jjc.gif|left|200px]]<br /><applet load="1jjc" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1jjc, resolution 2.60&Aring;" />
 '''Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese'''<br />
 ==Overview==
-The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus, thermophilus, a class II aminoacyl-tRNA synthetase, complexed with, phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution., Crystals of native PheRS were soaked in a solution containing, phenylalanine and ATP in the presence of Mn(2+) ions. The first step of, the aminoacylation reaction proceeds within the crystals, resulting in, Phe-AMP formation at the active site. Specific recognition of the, phenylalanine portion of the Phe-AMP is achieved by interactions of the, phenyl ring of Phe-AMP with two neighbouring residues, Phealpha258 and, Phealpha260. No manganese ions were observed within the active site; their, role in the formation of the transition state may be assigned to a number, of polar residues and water molecules. In the anomalous Fourier difference, map, a divalent metal ion was detected at the interface of the alpha- and, beta-subunits at a short distance from motif 3 residues participating in, the substrate binding. A sulfate ion, which was identified on the protein, surface, may mediate the interactions of PheRS with DNA. Visible, conformational changes were detected in the active-site area adjacent to, the position of the Phe-AMP, compared with the structure of PheRS, complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate)., Based on the known structures of the substrate-free enzyme and its, complexes with various ligands, a general scheme for the phenylalanylation, mechanism is proposed.
+The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution. Crystals of native PheRS were soaked in a solution containing phenylalanine and ATP in the presence of Mn(2+) ions. The first step of the aminoacylation reaction proceeds within the crystals, resulting in Phe-AMP formation at the active site. Specific recognition of the phenylalanine portion of the Phe-AMP is achieved by interactions of the phenyl ring of Phe-AMP with two neighbouring residues, Phealpha258 and Phealpha260. No manganese ions were observed within the active site; their role in the formation of the transition state may be assigned to a number of polar residues and water molecules. In the anomalous Fourier difference map, a divalent metal ion was detected at the interface of the alpha- and beta-subunits at a short distance from motif 3 residues participating in the substrate binding. A sulfate ion, which was identified on the protein surface, may mediate the interactions of PheRS with DNA. Visible conformational changes were detected in the active-site area adjacent to the position of the Phe-AMP, compared with the structure of PheRS complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate). Based on the known structures of the substrate-free enzyme and its complexes with various ligands, a general scheme for the phenylalanylation mechanism is proposed.
 ==About this Structure==
-JJC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with MN, SO4 and FA5 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JJC OCA].
+JJC is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=FA5:'>FA5</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJC OCA].
 ==Reference==
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 [[Category: Fishman, R.]]
 [[Category: Moor, N.]]
-[[Category: Safro, M.G.]]
+[[Category: Safro, M G.]]
 [[Category: FA5]]
 [[Category: MN]]
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 [[Category: thermus thermophilus]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:19:20 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:23:18 2008''