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3r67

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

    Title Crystal structure of a putative glycosidase (BT_4094) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3r67 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS47390,NP_813005.1, 324401
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 4
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.14 Rfactor 0.1521
    Waters
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    Solvent Content 42.65

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3r67

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    Protein Summary

     The hypothetical protein BT4094 determined with the resolution of 2.3A is a known 5-blade beta-propeller, very similar to glycosylase TM1225 with 22% seqID and no further function assignment [fig 1.]. 

     

    This fold represents a very 'asymmetric' beta-propeller in which 2 blades get partially 'unfolded', one of which builds a twisted beta-hairpin around the top opening of the propeller, the other surrounds the neighbor blades.

     

    The 2 misshaped blades also contribute with 2 short helical turns to the most out-sticking portion of the molecule, braking the otherwise 5-fold rotational symmetry along the central axis of the propeller. The 'Velcro' feature of each monomer, in which each N- and C-terminal is linked through a hydrogen bond network in order to stabilize the circular structure of the propeller, is preserved for this target. 4 molecules in the assymetric unit arrange themself in 2 pairs,

    perpendicular to each other, facing each others top opening with the most bind ligands, EDO molecules. 5 N-terminal residues are disordered. A long straight cavity crosses the central axis of the top portin of the propeller indicating a possible substrate binding site for elongated linear sugar molecules [fig. 2].

     

    This target has one particular feature, namely stacking of R258 with an R321, in a 'pi-pi' contact between their guanidinium groups{fig.3].

     

    This energetically favorable configuration doesn't involve any crystal contacts or solvent exposure. This R-pair is placed in the outer surface of the propeller, in a twisted groove

    which is possibly stabilized through a charge absorption from this configuration into the surrounding. Only few structures contain that kind of stacking:

    Glutathione-S-transferase (1GUH), hunam immunodeficiencyvirus type 1 protease (4HVP) and cellular receptor CD46 in PDB code 3EXW, 3EXV a,d 3FOY.

    The recently submitted coordinates of a new JCSG glycosyl hydrolase 3QC2, indciate the largest similarity to BT4094 target. The overall core rmsd over 365 aligned residues is 1.62A.

     

    The entire network of aromatic residues on each of the blades is conserved between these 2 structures. The 3 in one direction aligned EDO molecules located in the central negatively charged propeller cavity possibly simulate the substrate binding sites,which through their connections to the ASP364, GLU141, ASP142 might indicate the active residues participating in the hydrolysis act.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     CHIMERA-dimer.jpg
    2 monomers in the assymetric unit
    410.52 kB19:05, 18 Mar 2011cbtrameActions
     delphi-EDOpocket.jpg
    No description
    459.91 kB21:03, 18 Mar 2011cbtrameActions
     R321-R258_stack.jpg
    R-stack on the side of the propeller surrounded by aromatic residues
    371.83 kB21:19, 18 Mar 2011cbtrameActions
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