1vqm: Difference between revisions
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|PDB= 1vqm |SIZE=350|CAPTION= <scene name='initialview01'>1vqm</scene>, resolution 2.3Å | |PDB= 1vqm |SIZE=350|CAPTION= <scene name='initialview01'>1vqm</scene>, resolution 2.3Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</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=OMG:O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2'-METHYLURIDINE+5'-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PO2:HYPOPHOSPHITE'>PO2</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5'-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5'-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5'-MONOPHOSHATE'>UR3</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[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]], [[1vql|1VQL]], [[1vqn|1VQN]], [[1vqo|1VQO]], [[1vqp|1VQP]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vqm OCA], [http://www.ebi.ac.uk/pdbsum/1vqm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vqm RCSB]</span> | |||
}} | }} | ||
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[[Category: Schmeing, T M.]] | [[Category: Schmeing, T M.]] | ||
[[Category: Steitz, T A.]] | [[Category: Steitz, T A.]] | ||
[[Category: peptidyl transferase reaction]] | [[Category: peptidyl transferase reaction]] | ||
[[Category: protein-protein complex]] | [[Category: protein-protein complex]] | ||
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[[Category: rna-rna complex]] | [[Category: rna-rna complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:27:22 2008'' | ||
Revision as of 00:27, 31 March 2008
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| , resolution 2.3Å | |||||||
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| Ligands: | , , , , , , , , , , , , , , , , , | ||||||
| Related: | 1S72, 1JJ2, 1KQS, 1M90, 1Q7Y, 1Q81, 1Q82, 1Q86, 1QVF, 1QVG, 1FFK, 1FFZ, 1FGO, 1VQ4, 1VQ5, 1VQ6, 1VQ7, 1VQ8, 1VQ9, 1VQK, 1VQL, 1VQN, 1VQO, 1VQP
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
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