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2rdc

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

    Title Crystal structure of protein of unknown function (NP_951123.1) from Geobacter sulfurreducens at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 2rdc Target Id 372393
    Molecular Characteristics
    Source Geobacter sulfurreducens pca
    Alias Ids TPS1608,NP_951123.1 Molecular Weight 17380.76 Da.
    Residues 152 Isoelectric Point 5.90
    Sequence mqqptasvvsyvaeyhkatettmgrykkvieitghdevaaklleglidagtryfskvvemehrmasarf rldgeelreltetldrsrrlaheslisslhvfnryivkeygeelkeagieggifpkpeanrdriaiadw agelltgiyenrhr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.224
    Matthews' coefficent 1.97 Rfactor 0.193
    Waters 126 Solvent Content 37.56

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2rdc
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     

    Protein Summary

    The GSU0061 gene from Geobacter sulfurreducens encodes a putative C-terminal GTPase effector domain (GED) DUF3232 PF11554.  There is no exact sequence similarity match.  The fold assignment does not seem to be correct (SCOP)   The protein can be loosely associated with the  dynamin-related protein 5B-1.  The visual inspection of the structure of a bacterial dynamin-like protein lipid tube 2W6D [Ref] suggests that the GED domain of the structure is the closest functional and structural match for the given protein.  This annotation is widely open for discussion.

     

    FFAS shows remote homology of this family with a membrane-associated viral matrix protein gag (PF00540, score -92). Gag proteins are targeted to lipid rafts [Ref] and govern the assembly and release of virus particles, including capsid assembly, transport and budding.

    Genome context suggests functional association with TraD protein (GSU0062, score 0.6). TraD is a coupling protein, part of type IV secretion systems of plant, animal and human pathogens, and essential for DNA transfer in bacterial conjugation systems [Ref]. GSU0061 could have a DNA-binding or tethering role in this process.

    In the green alga Osteococcus tauri, the DUF3232 homolog is fused with a gene from the Sec34-like family (PF04136), involved in vesicle tethering to the Golgi compartment, supporting a role in lipid-binding/tethering/fission.

     

    To do: check electrostatic surface of this structure (both phospholipids and DNA are negatively charged), also conservation across homologs.

    Ligand Summary


    References

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