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3dcx

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

    Title Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J.Mol.Biol. 396 31-46 2010
    Site JCSG
    PDB Id 3dcx Target Id 380289
    Molecular Characteristics
    Source Shewanella sp. pv-4
    Alias Ids TPS7258,YP_001092950.1, PF08000 Molecular Weight 12895.21 Da.
    Residues 116 Isoelectric Point 5.66
    Sequence gnaaevnldelaqelgpimgdneqlalayrvirdmfvftnkrlilidkqgvtgkkvsyhsvpykaithf evetagtfdmdaelklwisgqkdplvkelkkgtdvvgiqktianfsl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.227
    Matthews' coefficent 2.45 Rfactor 0.184
    Waters 322 Solvent Content 49.70

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dcx
    1. Myosin 1G is an abundant class I myosin in lymphocytes whose localization at the plasma membrane depends on its ancient divergent pleckstrin homology (PH)
    G Patino-Lopez, L Aravind, X Dong, MJ Kruhlak - Journal of Biological , 2010 - ASBMB
     
    2. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
    Q Xu, A Bateman, RD Finn, P Abdubek - Journal of molecular , 2010 - Elsevier
     
    3. Bacterial toxin-antitoxin systems
    J Guglielmini, L Van Melderen - 2012 - landes.bjmu.edu.cn
     

    Protein Summary

    Gene Shew_0819 from Shewanella sp. pv-4 encodes the protein YP_001092950 that shares sequence similarity with the DUF1696 (PF08000) family from Pfam (E-value: 1.3e-68). It is the second solved structural representative of this family. Residues 2-125 of ZP_00539245.1 (PDB code: 3b77) also share sequence similarity to the DUF1696 (PF08000) family from Pfam (E-value: 0.063). This structure was also solved by JCSG and has it own entry.

    3dcx is a pentamer (See Figure 1 below). Each monomer within the pentamer is a Pleckstrin homology domain (PH domain), which in general uses a positive charge surface to interact with membrane. Structurally, 3dcx belongs to the proteins in the PH domain-like superfamily from SCOP, and it has its own family, BPHL domain family.

    According to SSM, the most similar structures are the GLUE domain of ESCRT-II with PDB codes: PDB:2dx5, chain A, which has a RMSD of 1.7 A for 99 residues with 15% sequence identity, Z=9;  and PDB:2hth, chain B, which has a RMSD of 1.9 A for 129 residues with 14% sequence identity, Z=9. However,  3dcx share smore sequence similarity with the PH domain of ZP_00539245.1 (PDB:3b77, which has a RMSD 3.0 A for 109 residues with 24% sequence identity according to FATCAT, DALI Z=10). DALI top hit is with another DUF1696 PDB:3hsa (Z=16).

     

    For many PH domains, the electrostatic potential is bipolar, with a positive lobe enveloping the open end of the beta-barrel. In that region, the relevant loops (b1/b2, b3/b4 and b6/b7) are highly variable with respect to length and sequence and provide tailored interaction with specific phospholipids (DiNitto 2006).

     

    In 3dcx, the b6/b7 loop, containing the highly conserved Lys-99, is responsible for creating a positive center at the pore of the pentamer surrounded by a strong negative potential, which could serve in orienting a ligand via long-range electrostatic steering (Fig. 1). On the opposite side of the complex, the pore is lined by the strictly conserved Lys-49 while at the periphery, two pairs of highly conserved basic residues (Lys-62, Lys63 and Lys-107, Lys-108) create a basic ring around the pentamer (Fig. 1).

     

    3dcx_isosurface1.png

     

    3dcx_isosurface2.png

    Figure 1: Electrostatic isosurfaces of the 3dcx pentamer contoured at +2kT (positive, in blue) and -2kT (negative, in red). On the top, the side facing the helices, bottom, the side facing the beta-strands. 

    Ligand Summary

    Reviews

    References

     

    No references found.

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    663.75 kB00:41, 13 Dec 2008tinabActions
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