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{{Large structure}}
==The structure of the transition state analogue "DCSN" bound to the large ribosomal subunit of haloarcula marismortui==
{{STRUCTURE_1vql|  PDB=1vql  |  SCENE=  }}
<StructureSection load='1vql' size='340' side='right' caption='[[1vql]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
===The structure of the transition state analogue "DCSN" bound to the large ribosomal subunit of haloarcula marismortui===
== Structural highlights ==
{{ABSTRACT_PUBMED_16285925}}
<table><tr><td colspan='2'>[[1vql]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VQL FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=TSE:THIOPHOSPHONOACETIC+ACID'>TSE</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s72|1s72]], [[1jj2|1jj2]], [[1kqs|1kqs]], [[1m90|1m90]], [[1q7y|1q7y]], [[1q81|1q81]], [[1q82|1q82]], [[1q86|1q86]], [[1qvf|1qvf]], [[1qvg|1qvg]], [[1ffk|1ffk]], [[1ffz|1ffz]], [[1fgo|1fgo]], [[1vq4|1vq4]], [[1vq5|1vq5]], [[1vq6|1vq6]], [[1vq7|1vq7]], [[1vq8|1vq8]], [[1vq9|1vq9]], [[1vqk|1vqk]], [[1vqm|1vqm]], [[1vqn|1vqn]], [[1vqo|1vqo]], [[1vqp|1vqp]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vql OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vql RCSB], [http://www.ebi.ac.uk/pdbsum/1vql PDBsum]</span></td></tr>
<table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vq/1vql_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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==
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<ref>PMID:16285925</ref>
[[1vql]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQL OCA].
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Ribosomal protein L10|Ribosomal protein L10]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosomal protein L11|Ribosomal protein L11]]
== References ==
*[[Ribosomal protein L13|Ribosomal protein L13]]
<references/>
*[[Ribosomal protein L14|Ribosomal protein L14]]
__TOC__
*[[Ribosomal protein L2|Ribosomal protein L2]]
</StructureSection>
*[[Ribosomal protein L3|Ribosomal protein L3]]
*[[Ribosomal protein L5|Ribosomal protein L5]]
*[[Ribosomal protein L6|Ribosomal protein L6]]
*[[Ribosomal protein L7|Ribosomal protein L7]]
 
==Reference==
<ref group="xtra">PMID:016285925</ref><references group="xtra"/>
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
[[Category: Schmeing, T M.]]
[[Category: Schmeing, T M.]]

Revision as of 00:03, 30 September 2014

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

Structural highlights

1vql is a 31 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , , , ,
NonStd Res:, , , , ,
Related:1s72, 1jj2, 1kqs, 1m90, 1q7y, 1q81, 1q82, 1q86, 1qvf, 1qvg, 1ffk, 1ffz, 1fgo, 1vq4, 1vq5, 1vq6, 1vq7, 1vq8, 1vq9, 1vqk, 1vqm, 1vqn, 1vqo, 1vqp
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell. 2005 Nov 11;20(3):437-48. PMID:16285925 doi:http://dx.doi.org/10.1016/j.molcel.2005.09.006

1vql, resolution 2.30Å

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