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3gyd

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

    Title Crystal structure of cyclic nucleotide-binding domain (YP_546034.1) from Methylobacillus flagellatus KT at 1.79 A resolution. To be published
    Site JCSG
    PDB Id 3gyd Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS20178,YP_546034.1, 2.60.120.10, 85255
    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 1.94 Rfactor 0.168
    Waters
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    Solvent Content 36.71

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3gyd

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    Protein Summary

    Pfam update:This protein is now in family Family: cNMP_binding (PF00027)

    Gene Mfla_1926 from Methylobacillus flagellatus KT encodes the YP_546034 protein that belongs to cyclic nucleotide mono phosphate (cNMP) binding family ( PF00027).

    The protein structure, 3gyd, assembles as a dimer in the crystallographic asymetric unit, which is also a biological unit. Each monomer contain an anti-cAMP molecule in the cAMP binding site.

     

    dimer_asu.png

    Fig 1. Bilogical dimer of 3gyd.

     

    Dali hits many cyclic nucleotide binding proteins, either c-AMP free [

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    (Z=17.3, 3.4A rmsd, 23 %id),
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    (Z=16.4, 2.7 A rmsd, 10 %id) and
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    (Z=15.9, 3.8A rmsd, 16 %id)] or c-AMP bound forms [
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    (Z=15.5, 3.6A, 19 %id),
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    (Z=15.5, 3.8A, 19 %id) and
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    (Z=15.5, 3.3A, 20 %id)). The superpositions of 3gyd with 3d0s and 1i6x are shown in the figures below.

    super_3d0s_A (1).png

    Fig 2. Superposition of 3gyd with 3d0s. The cAMP of 3gyd is shown in red. 3d0s (yellow) is a free-cAMP form. It contains extra Crp domain (PF00325 Link out to PFAM:PF00325; Bacterial regulatory proteins, crp family) compared to 3gyd.

     

    super_1i6x.png

    Fig 3. Superposition of 3gyd (green) with 1i6x (orange). Both structures contain anti-cAMP. In addition, 1i6x contains extra Crp domain ( PF00325 Link out to PFAM:PF00325; Bacterial regulatory proteins, crp family).

     

    Most of the residues that interact with cAMP are conserved in both 3gyd and 1i6x structures. However, two key residues interacting the N6 atom of cAMP are different. They are Ser 155-A and Tyr 156-B in the 3gyd structure (green) compared to Thr127-A and Ser128-B in the 1i6x structure (orange), as shown in the figure below.

     

    Interestingly, the cAMP interaction with the Ser155-A and Tyr156-B residues of 3gyd is a bit different between the A and B chains. The N6 atom of cAMP-B interacts with Thr127-B and Ser128-A. However, cAMP-A no longer interacts with the Tyr 156-B as shown below. Tyr156-B is now pushed away.  

     

    CMP_active_1i6x_label.png

     

    Fig 4. cAMP interacting residues in 3gyd (green) and 1i6x (orange).

     

    References

     

     

     

     

     

    Passner, J.M., Schultz, S.C., Steitz, T.A. (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution. J.Mol.Biol. 304: 847-859 View PubMed Abstract at NCBI

    Ligand Summary

     

    Each monomer of the 390943 contains a adenosine-3p,5p-cyclic-monophoshate (CMP) in the active site.

    This is the first CMP bound structure from PSI centers.

    Reviews

    References

     

    No references found.

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    Files (17)

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    181.38 kB21:27, 7 Apr 2009gyewonActions
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    152.29 kB06:30, 15 Apr 2009gyewonActions
     super_3d0s_A (1).png
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    207.42 kB23:33, 6 Apr 2009gyewonActions
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