1VQ5

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.

Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., Steitz, T.A.

(2005) Mol Cell 20: 437-448

  • DOI: 10.1016/j.molcel.2005.09.006
  • Primary Citation of Related Structures:  
    1VQK, 1VQ9, 1VQ8, 1VQ5, 1VQ4, 1VQP, 1VQO, 1VQM, 1VQL

  • PubMed Abstract: 

    • 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 substr ...

    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.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2P A240Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3P B338Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E C246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5P D177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6P E178Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AE F120Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG G348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10E H171Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13P J145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14P K132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15P L165Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
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50S Ribosomal Protein L15E M194Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18P N187Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18e O116Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19E P149Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21e Q96Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
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50S ribosomal protein L22P R155Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
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50S ribosomal protein L23P S85Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24P T120Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24E U66Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29P V71Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30P W154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31e X92Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32E Y241Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37Ae Z83Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37e 157Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39e 250Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44E 392Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11P I162Haloarcula marismortuiMutation(s): 0 
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal rna02922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNA9122Haloarcula marismortui
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    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(*(DC)P*(DC)P*(5AA)P*(2OP)P*(PO2)P*AP*C*C)-3')48N/A
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CD
    Query on CD
    Download Ideal Coordinates CCD File 
    1, 3, O, U, Z
    		CADMIUM ION
    Cd
    WLZRMCYVCSSEQC-UHFFFAOYSA-N    		 Ligand Interaction
    K
    Query on K
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    0
    		POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N    		 Ligand Interaction
    CL
    Query on CL
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    0, 3, A, B, J, L, M, N, O, R, Y
    		CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    MG
    Query on MG
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    0, 2, 3, 4, 9, A, B, K, T, Y
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    NA
    Query on NA
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    0, 9, A, B, C, H, J, L, M, Q, R, S
    		SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.237 
    • R-Value Work: 0.197 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 211.788α = 90
    b = 300.614β = 90
    c = 573.363γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    CNSrefinement
    HKL-2000data reduction
    CNSphasing

    Structure Validation

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    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2005-11-29
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Non-polymer description, Version format compliance