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The Open Protein Structure Annotation Network
PDB Keyword
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388639

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

    Site JCSG
    Status Diffraction-quality Crystals
    Target Id 388639
    Molecular Characteristics
    Source Eubacterium rectale
    Alias Ids TPS7537, Molecular Weight 25297.99 Da.
    Residues 219 Isoelectric Point 5.99
    Sequence msfenyfplwndlntaqkklisdnlitqhvkkgtiihngnmdctglllvksgqlrtyilsdegreitlyrlfdmdm cllsascimrsiqfevtieaekdtdlwiipaeiykgimkdsapvanytnelmatrfsdvmwlieqimwksldkrv asflleetsiegtnelkithetianhlgshrevitrmlryfqveglvklsrgkitildskrletlqrs
      BLAST   FFAS
    Ligand Information
    Ligands
    Metals
    Google Scholar output for

    Protein Summary

    The target 388639 (RER070207001219) is a two domain structure linked by a helix. The protein belongs to PFAMs PF00027 and PF00325.  PF00027 proteins have a cyclic nucleotide-binding domain, where as PF00325 are bacterial regulatory proteins (crp family). Both of these domains bind DNA and suggest that
    the target 388639 should bind DNA too.

    GD10876A.png

    Fig 1. Monomer structure of the target 388639 showing two domains linked by a helix.


    GD10876A_dimer.png
    Fig 2. The protein most likey exists as a dimer as shown by the crystal packing structure.


    Structural Homologs: A SSM search returns several hits, e.g. 2zcw 2coh 1o3r 2cgp 1o3s 1o3q 2gau 1zrf. A few of these structures are shown superposed on the target in Fig 3. Similarly, FFAS page lists several significant homologs for this target too, of which 1g6n, 1o5l, and 2gau top the list.

    all.pngFFAS_all.png

     

                                             A                                                                  B 

    Fig 3. Superposition of structural homologs. A. SSM hits: 388639 (green), 1o3r (cyan), 1o3s (magenta), 2cgp (yellow), 2coh (pink), and 2zcw (blue). The bound DNA and CMP in other structures have also been shown. B. FFAS hits: 388639 (green), 1o5l (magenta), and 2gau (yellow).

    Most of these proteins are DNA binding proteins involved in gene regulatory functions. By structural homology, this target should have some similar function. Indeed, based on the comparison with 1o3s (Fig 4), we see that the dimer of this target is poised to bind DNA (Fig 5), although DNA or CMP are absent in the crystal structure.

    GD10876A_1o3s.png
    Fig 4. Comparison of target 388639 (green) with 1o3s (magenta). The CMP and DNA in 1o3s have been shown to highlight the corresponding binding site in the target.


    GD10876A_DNAbinding.png
    Fig 5. Hypothetical model of DNA binding by the dimer of this target.




    References

     Yau KW; , Proc Natl Acad Sci USA 1994;91:3481-3483.: Cyclic nucleotide-gated channels: an expanding new family of ion channels.

    Ligand Summary

    Reviews

    References

     

    No references found.

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