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    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


    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).





    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




    No references found.

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