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1dd5

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic. Science 286 2349-2352 1999
    Site OTHER
    PDB Id 1dd5 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS19940, TM1399
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.86 Rfactor 0.23
    Waters
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    Solvent Content 68.00

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    Ligand Information
    Ligands ACY (ACETIC) x 2
    Metals

    Jmol

     
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    Google Scholar output for 1dd5

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    Protein Summary

    The TM1399 gene of Thermotoga maritima encodes a ribosome recycling factor (RRF), a well conserved protein among most organisms and an essential protein among prokaryotes. RRF acts in concert with elongation factor G (EF-G) to dissociate ribosome subunits at the end of protein translation. The mechanism of action of ribosome disassembly is currently unknown. The TM1399 RRF structure, the first structure of a RRF to be solved, shows an 'L shape' characteristic of tRNA suggesting that RRF could act as a tRNA mimic (1). Subsequent studies of RRF bound to the ribosome dispute this hypothesis, suggesting that RRF acts to stabilize the ribosome with a subsequent conformational change in RRF required for ribosome subunit splitting (2).

    The TM1399 RRF consists of two domains (Fig. 1). Domain I is a three-helix bundle (residues 2-30 and 105-185) with the helices tightly packed against each other. Domain II is a β/α/β sandwich (residues 31-104). A structural superposition with the structure of yeast tRNAPhe (3) shows an overall similarity in both shape and dimensions suggesting that the mechanism of action of RRF might involve protein-tRNA mimicry.



    Figure 1. Ribbon diagram of RRF (in gray) superposed with yeast tRNAPhe (PDB id: 4TNA, in blue). The domain structure of RRF is indicated. Linker regions are shown in orange.

    RRF domain I was subsequently shown to bind along the 50S ribosome A and P sites as opposed to mimicking the anticodon step loop (4). NMR relaxation experiments (5) suggest that the linker regions between the domains I and II (residues 27-33 and 101-106) are flexible. Comparison of RRF crystal structures also shows a variability in the angle between the two domains (6), suggesting that interactions between RRF and EF-G might be required to constrain this domain in a specific orientation. Further structural snapshots along the translation pathway will be required before the mechanism of action of RRF can be fully elucidated.

    Ligand Summary

    Reviews

    References

     

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