1vqk

The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of haloarcula marismortui

spinqualitylabelsall models 1vqk, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1vqk is a 10 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.3Å Ligands: 1MA, ACA, CD, CL, K, MG, NA, OMG, OMU, PSU, SR, UR3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RL21_HALMA This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosome 3D structures

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