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Structure of IDP90549

Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A.

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CSGID target
IDP90549 
PDB Id
3L92 (NCBI MMDB) 
Authors
Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 04, 2010 
Release Date
Jan 19, 2010 

Annotation

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Description
Phosphopantetheine adenylyltransferase (PPAT) catalyzes the conversion of ATP and pantetheine 4'-phosphate (PhP) to pyrophosphate (PPi) and 3'-dephospho-CoA (dPCoA). This reaction is known as the penultimate step in the coenzyme A (CoA) biosynthetic pathway and has been shown to be a rate-limiting step in the biosynthesis of CoA. PPAT is part of the nucleotidyltransferase α/β phosphodiesterase superfamily, which includes nicotinate mononucleotide adenylyltransferase (NMAT) and glycerol 3-phosphate cytidylyltransferase. PPAT was identified as an attractive antimicrobial drug target in the CoA biosynthesis pathway due to its broad-spectrum nature and the lack of similarity between bacterial and human enzymes. 
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
    COA coenzyme A biological

    Structure information

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    Unit cell parameters

    Space Group
    H 3 2  
    Unit Cell

    a=114.82Å, b=114.82Å, c=119.07Å
    α=90.00, β=90.00, γ=120.00  
    Solvent content
    70.77  
    Matthews coefficient
    4.21  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    38.30-1.89Å (1.94-1.89Å)  
    Rall(%)
    16.5  
    Rwork(%)
    16.4 (23.7)  
    Rfree(%)
    19.2 (28.3)  
    Num. observed reflections
    24310 (1776)  
    Num. Rfree reflections
    1239 (89)  
    Completeness(%)
    100.0 (99.8)  

    Model parameters

    Num Atoms
    1595  
    Num Waters
    166  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    26.900  
    RMSD bond length (Å)
    0.020  
    RMSD bond angle
    1.866°  
    Filename uploaded
    idp90549_CoA.pdb (uploaded on Jan 18, 2010 2:03 PM)  
    Inserted
    Jan 18, 2010