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Structure of IDP90523

Pantoate-beta-alanine ligase from Yersinia pestis in complex with pantoate.

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CSGID target
IDP90523 
PDB Id
3Q12 (NCBI MMDB) 
Authors
J.Osipiuk,N.Maltseva,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Dec 16, 2010 
Release Date
Feb 02, 2011 

Annotation

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Description
Pantoate-beta-alanine ligase, also known as panthotenate synthetase, catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine which is the last step of pantothenate biosynthesis. The reaction is Mg2+-dependent. Pantothenate (vitamin B5) is a key precursor of the 4-phosphopantetheine moiety of coenzyme A (CoA) and the acyl carrier protein (ACP) which are essential for cell growth. Microorganisms and plants synthesize pantothenate, while animals obtain this nutrient from their diet. The pantothenate-biosynthetic pathway offers a potential target for the design of new drugs against microbial pathogens.  
Functional assignment
Ligase 
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
    CL chloride ion crystallization
    PAF pantoate biological

    Structure information

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    Unit cell parameters

    Space Group
    P 1  
    Unit Cell

    a=44.73Å, b=77.05Å, c=98.76Å
    α=100.67, β=95.33, γ=94.43  
    Solvent content
    52.39  
    Matthews coefficient
    2.58  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    36.69-1.58Å (1.62-1.58Å)  
    Rall(%)
    15.2  
    Rwork(%)
    15.0 (27.2)  
    Rfree(%)
    19.5 (33.9)  
    Num. observed reflections
    153765 (5417)  
    Num. Rfree reflections
    7688 (271)  
    Completeness(%)
    87.2 (41.5)  

    Model parameters

    Num Atoms
    10600  
    Num Waters
    1154  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    21.120  
    RMSD bond length (Å)
    0.018  
    RMSD bond angle
    1.668°  
    Filename uploaded
    idp90523_paf.pdb (uploaded on Dec 16, 2010 4:54 PM)  
    Inserted
    Dec 16, 2010