1vqm: Difference between revisions

Revision as of 16:37, 21 February 2008

The structure of the transition state analogue "DAN" bound to the large ribosomal subunit of haloarcula marismortui

OverviewOverview

Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

About this StructureAbout this Structure

1VQM is a Protein complex structure of sequences from Haloarcula marismortui with , , , , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction., Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA, Mol Cell. 2005 Nov 11;20(3):437-48. PMID:16285925

Page seeded by OCA on Thu Feb 21 15:37:37 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1vqm.gif|left|200px]]<br /><applet load="1vqm" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1vqm.gif|left|200px]]<br /><applet load="1vqm" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1vqm, resolution 2.3&Aring;" />
 '''The structure of the transition state analogue "DAN" bound to the large ribosomal subunit of haloarcula marismortui'''<br />
 ==Overview==
-Peptide bond formation is catalyzed at the peptidyl transferase center, (PTC) of the large ribosomal subunit. Crystal structures of the large, ribosomal subunit of Haloarcula marismortui (Hma) complexed with several, analogs that represent either the substrates or the transition state, intermediate of the peptidyl transferase reaction show that this reaction, proceeds through a tetrahedral intermediate with S chirality. The oxyanion, of the tetrahedral intermediate interacts with a water molecule that is, positioned by nucleotides A2637 (E. coli numbering, 2602) and, (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions, observed in the PTC that could directly promote catalysis. The A76 2', hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group, and could facilitate peptide bond formation by substrate positioning and, by acting as a proton shuttle between the alpha-amino group and the A76 3', hydroxyl of the peptidyl-tRNA.
+Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.
 ==About this Structure==
-VQM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with MG, K, NA, CD, CL and SR as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VQM OCA].
+VQM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CD:'>CD</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=SR:'>SR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQM OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Haloarcula marismortui]]
 [[Category: Protein complex]]
-[[Category: Schmeing, T.M.]]
+[[Category: Schmeing, T M.]]
-[[Category: Steitz, T.A.]]
+[[Category: Steitz, T A.]]
 [[Category: CD]]
 [[Category: CL]]
@@ Line 27: / Line 27: @@
 [[Category: rna-rna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:03:33 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:37:37 2008''