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Structure of IDP00348

1.95 Angstrom crystal structure of a bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase (aroA) from Listeria monocytogenes EGD-e

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CSGID target
IDP00348 
PDB Id
3NVT (NCBI MMDB) 
Authors
Halavaty, A.S. Light, S.H. Minasov, G. 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
Jul 08, 2010 
Release Date
Jul 28, 2010 

Annotation

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Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. 3-deoxy-7-phosphoheptulonate DAHP synthase catalyzes the conversion of phosphoenolpyruvate and D-erythrose 4-phosphate to DAHP, the first step in the shikimate pathway. Chorismate mutase catalyzes the conversion of chorismate, the shikimate pathway’s endproduct, to prephenate. Prephenate is a precursor for the aromatic amino acids phenylalanine and tyrosine. While structures of individual DAHP and chorismate mutase domains have been previously solved, this structure is the first to characterize this natural bifunctional protein which is found in a subset of bacteria. This structure reveals that the DAHP synthase domains are assembled into their typical physiological tetrameric state. The N-terminal chorismate mutase domains emerge from either side of the tetramer and after a lengthy linker region form a pair of dimers which sandwich the tetrameric core. The linker region between the DAHP and chorismate mutase domains acts differently within the two molecules within the asymmetric unit - a result which may be due to crystal packing.  
Functional assignment
 
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
    MN unknown biological
    ACT acetate ion

    Structure information

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    Unit cell parameters

    Space Group
    C 1 2 1  
    Unit Cell

    a=111.57Å, b=111.79Å, c=81.05Å
    α=90.00, β=127.63, γ=90.00  
    Solvent content
    47.79  
    Matthews coefficient
    2.36  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.04-1.95Å (2.00-1.95Å)  
    Rall(%)
    15.6  
    Rwork(%)
    15.4 (19.2)  
    Rfree(%)
    19.8 (22.7)  
    Num. observed reflections
    57304 (4046)  
    Num. Rfree reflections
    2922 (190)  
    Completeness(%)
    99.5 (95.6)  

    Model parameters

    Num Atoms
    5330  
    Num Waters
    756  
    Num Hetatoms
    775  
    Model mean isotropic B factor (Å2)
    43.560  
    RMSD bond length (Å)
    0.010  
    RMSD bond angle
    1.254°  
    Filename uploaded
    3NVT.pdb (uploaded on Sep 18, 2010 3:48 PM)  
    Inserted
    Jul 13, 2010