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The Open Protein Structure Annotation Network
PDB Keyword
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3h51

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

    Title Crystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3h51 Target Id 396520
    Molecular Characteristics
    Source Xanthomonas campestris pv. campestris str. atcc 33913
    Alias Ids TPS25430,NP_636218.1, 3.10.450.50, 424148 Molecular Weight 17037.26 Da.
    Residues 155 Isoelectric Point 6.09
    Sequence ggvmhytdkaalpadgearevaalfdtwnaalatgnphkvadlyapdgvllptvsnevrasreqienyf emfltkkpkgvinyrtvrlldddsavdagvytftltdkngkksdvqarytfvyekrdgkwliinhhssa mpevdtatataavtkak
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.215
    Matthews' coefficent 2.32 Rfactor 0.179
    Waters 251 Solvent Content 46.96

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam update:This protein is now in family PF08332.3 CaMKII_AD CL0051 along with other structures.

    NP_636218.1 from Xanthomonas campestris encodes a protein which belongs to Pfam; PF08332; Calcium/calmodulin dependent protein kinase II Association (CaMKII_AD) found at the C-terminus of the CaMKII. CaMKII_AD is a member of clan Nuclear Transport Factor 2 NTF2 (CL0051) which contains the following 8 members: (CaMKII_AD  DUF1348 LEH MecA_N NTF2 Ring_hydroxyl_B Scytalone_dh SnoaL)

     

    dimer_PX11702A.png

    Fig 1. The dimer of NP_636218.1 structure.

    The PDB hits of structural homologs by DALI are uncharacterized protein (PDB: 3cnx TOPSAN and 3b8lTOPSAN ), ketosteroid isomerase-like protein (PDB: 3d9r TOPSAN) and NTF2 proteins (PDB: 1qma, 1gy6, 1oun, 1u5o, 1ar0, 1ask, 1jb2, 1gy5, 1jb4 and 1a2k).

     

    Superposition of the NP_636218.1 with 3cnx, 1oun are shown in the figure below. The structures of these proteins are very similar.

       super_3cnx.pngsuper_1oun.png

     Fig 2. Superposition of NP_636218.1 with 3cnx (light blue) and 1oun (pink). Please notice that the dimer formation of 3cnx is very similar to that of NP_636218.1.

     

    A putative binding site which is conserved in the different isoforms of CaMKII_AD from different organismss, is found in the NP_636218.1. This is formed by His153, Tyr119, Ser155, Thr72 and Tyr87 (yellow sticks), and those residues are not conserved inthe CaMKII_AD. An unidentified ligand (UNL, red spheres) is found in this presumable active site of both A and B chains.

    UNL (2).png 

     Fig 3. Presumable active site of NP_636218.1. The omit map (1 sigma) of UNL is shown as blue mesh. (It resembles an Acetate ion.) Residues Tyr87, Thr72, Ser 153, Tyr119, and His153 are shown clockwise, right to left.

    References

    Bayliss, R.,  Leung, S.W.,  Baker, R.P.,  Quimby, B.B.,  Corbett, A.H.,  Stewart, M. (2002) Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats. EMBO J. 21: 2843-2853
       View PubMed Abstract at NCBI

    Bullock, T.L.,  Clarkson, W.D.,  Kent, H.M.,  Stewart, M. (1996) The 1.6 angstroms resolution crystal structure of nuclear transport factor 2 (NTF2). J.Mol.Biol. 260: 422-431

    View PubMed Abstract at NCBI

    Ligand Summary

    Reviews

    References

     

    No references found.

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