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The Open Protein Structure Annotation Network
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4e5v

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

    Title Crystal structure of a Putative thua-like protein (PARMER_02418) from Parabacteroides merdae ATCC 43184 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 4e5v Target Id 419184
    Molecular Characteristics
    Source Parabacteroides merdae atcc 43184
    Alias Ids TPS66837,ZP_02032405.1 Molecular Weight 31645.93 Da.
    Residues 280 Isoelectric Point 6.83
    Sequence rkpiktllitgqnnhnwqvshvvlkqilensgrfdvdfvispeqgkdmsgfvldfspyqlvvldyngds wpeetnrrfleyvqngggvviyhaadnafskwpefnricalggwegrnensgpyvywkdgklvkdssag pggshgrqheyvlngrdkvhpvvkglplkwrhakdelydrmrgpgnirdilytaysdketngsgreepl vftvdygnarifhtmlghagattedniamqctgfqvlllrgaewaatgkvtqkvpkdfptettcsyrkd yken
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.75 Rfree 0.1740
    Matthews' coefficent 2.19 Rfactor 0.1478
    Waters 647 Solvent Content 43.96

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     

     

     

    TARGET: SP13677A /172196 : ZP_02032405.1

     

     

     

    ThuA-like protein fold of Parabacteroides merdae (ATCC 43184) 34.4kDa heavy hypothetical protein according to FFAS server has 15% sequence ID with similar protein from Bacillus Stearothermophilus. This protein with unknown function represents, despite a strong interaction between the 2 protomers in ASU, according to PISA, a monomer. A beta-sheet/alpha fold of this protein has an active side with a Zn ion on its surface coordinated by 3 histidines (249, 116, 39), one tyrosine (200) and one glutamic acid (198), one EDO and one water molecule. The 3 histidines are positioned roughly in one plane, spanning a triangle which builds a positive charged opposition to the negatively charged remaining coordinating residues surrounding the Zn ion. Glu198 is positioned in the vicinity of an antiparallel wide type of beta-bulge, constituted by residues Glu172,Ala195 and Lys196.

     

     

    The most similar pdb structure 1T0B, contains also a Zn ion in the same position as in ZP_02032405.1. In 1T0B the Zn ion is coordinated by 2 histidines, 1 Glu and 3 water molecules, both of the residues are conserved. The remaining coordinating residues from ZP_02032405.1 target are also conserved in 1T0B.

     

     

    Overall the entire fold is strongly conserved with exception for the C-terminal strand and beta-hairpin (residues 279-304) which in our target run in 180degree opposite direction, holding on to the globular portion of the molecule, whereas in 1T0B that portion departs from the main fold and builds a ~50A 'loose end' winding around the neighbor molecule, implicating a dimerization. It is possible, that that part of the molecule possesses such a flexible feature, which in our target is suppressed and influenced by a rich presence of the EDO ligands coordinating the C-terminal of the monomer.

     

     

    The structure contains 5 different antiparallel beta-bulges, usually known for their catalytic features.

     

    Dali Server results in a rmsd of 2.6A for the 1T0B (equally without function assignment) structural similarity to our target with 17% seqID. Even higher sequence ID of 18% is assigned to the putative cytoplasmic protein 2GK3, for which the rmsd equals 2.9A.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (1)

    FileSizeDateAttached by 
    dimer.tif
    dimer with active center
    4.54 MB18:47, 14 Feb 2012cbtrameActions
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