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Structure of IDP90611

1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP

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CSGID target
IDP90611 
PDB Id
3LV8 (NCBI MMDB) 
Authors
Halavaty, A.S. Minasov, G. Dubrovska, I. Winsor, J. Shuvalova, L. Kwon, K. Anderson, W.F. Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Feb 19, 2010 
Release Date
Mar 02, 2010 

Annotation

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Description
A thymidylate kinase catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP). This enzyme from Vibrio cholerae O1 biovar eltor str. N16961 was co-crystallized with dTMP and ADP. Crystal diffracted to 1.8 Å resolution and a molecular replacement solution was obtained using the structure of the Escherichia coli thymidylate kinase with the bisubstrate inhibitor TP5A (PDB ID 4TMK) as a model. Analysis of the two ligand-binding sites in the initial model of the V. cholerae protein revealed a positive peak close to the dTMP’s phosphate group. This density clearly indicated presence of an additional phosphate group, which however seemed to be linked to the dTMP’s phosphate group. Knowing the protein’s function and assuming cellular uptake of dTDP can occur during purification procedure, this nucleotide was modeled with half occupancy into the dTMP-binding site. No negative difference density was observed after refinement. That is, the crystal structure of the V. cholerae thymidylate kinase has been solved in complex with dTMP, dTMDP and ADP. Two calcium ions interact with the nucleotides. Four more calcium ions are found associated with the protein as a result of presence of 0.2 M CaCl2 in the crystallization condition.  
Functional assignment
Transferase 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    secondary structure, N to C, molecule

    Ligands

    Ligand code Name Ligand type
    TMP thymidine-5'-phosphate biological
    TYD thymidine-5'-diphosphate biological
    ADP adenosine-5'-diphosphate
    CA calcium ion
    CL chloride ion

    Structure information

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    Unit cell parameters

    Space Group
    P 43 3 2  
    Unit Cell

    a=112.97Å, b=112.97Å, c=112.97Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    45.87  
    Matthews coefficient
    2.27  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    30.00-1.80Å (1.85-1.80Å)  
    Rall(%)
    16.6  
    Rwork(%)
    16.4 (20.5)  
    Rfree(%)
    20.4 (26.4)  
    Num. observed reflections
    23239 (1615)  
    Num. Rfree reflections
    1185 (92)  
    Completeness(%)
    99.4 (95.8)  

    Model parameters

    Num Atoms
    1668  
    Num Waters
    287  
    Num Hetatoms
    371  
    Model mean isotropic B factor (Å2)
    24.440  
    RMSD bond length (Å)
    0.011  
    RMSD bond angle
    1.494°  
    Filename uploaded
    3LV8.pdb (uploaded on Sep 17, 2010 5:51 PM)  
    Inserted
    Feb 25, 2010