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The Open Protein Structure Annotation Network
PDB Keyword
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2g42

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

    Title Crystal structure of hypothetical protein (tm0693) from Thermotoga maritima at 2.28 A resolution. To be published
    Site JCSG
    PDB Id 2g42 Target Id
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    Related PDB Ids 2fzt 
    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1922,TM0693
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.18 Rfactor 0.203
    Waters
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    Solvent Content 43.23

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2g42
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    The gene TM0693 from Thermotoga maritima encodes the NP_228502 protein from the DUF3214 group (PF11499). A genome-wide BLAST sequence alignment search indicated close sequence identity (33%) of the  TM0693 to a S15 RNA-binding protein from Thermosipho africanus TCF52B (YP_002334005).  The small (30S) bacterial ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Other homologous proteins are ATP synthase H subunit from Ferroglobus placidus DSM 10642 (36% over 73 residues) and Rad50 zinc hook motif family from Thermococcus barophilus MP (32% over 77 residues).

    The 2g42 structure belongs to the class of all alpha proteins and reveals a methionine synthase domain-like fold (SCOP47643).  Another crystal structure of the same protein is available 2FZT. Both show an identical dimeric structure in different crystal forms, suggesting that a dimer is the biologically relevant unit. DALI returns only weak hits with  the glycil-tRNA synthetase 1j5w (Z=6), the spectrin repeat 3edu (Z=6) or the ribosome recycling factor 1eh1 (Z=6). According to DALI, the crystal structure of S15 from Thermus thermophilus in complex with rRNA 1DK1 shows some structural similarity (Z=3) to 2g42 [Ref]. Thus, it is tempting to speculate that TM0693 might encode a S15 rRNA-binding related protein. Hovever, S15 is a monomer and the three-dimensional comparison shows marked differences between 2g42 and free or DNA-bound S15, in contrast to the high structural similarity among the many S15 proteins present in the pdb.

    Ligand Summary



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