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Structure of IDP90722

Crystal Structure of Biotin Carboxylase-beta-gamma-ATP Complex fromCampylobacter jejuni

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CSGID target
IDP90722 
PDB Id
3OUU (NCBI MMDB) 
Authors
N.Maltseva,Y.Kim,M.Makowska-Grzyska,R.Mulligan,L.Papazisi,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Sep 15, 2010 
Release Date
Oct 20, 2010 

Annotation

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Description
Biotin carboxylase, encoded by the accC gene, catalyzes the first step in fatty acid biosynthesis. It catalyzes the ATP-dependent transfer of carboxyl group from bicarbonate to biotin molecule of biotin carboxylase carrier protein (BCCP) . During second part of reaction transcarboxylase transfers the carboxyl group from carboxybiotinylated BCCP to acetyl-CoA to form malonyl-CoA and regenerate biotinylated BCCP. The formation of malonyl-CoA in turn controls the rate of fatty acid metabolism. Crystal structure of biotin carboxylase-beta-gamma-ATP complex from Campylobacter jejuni was solved at 2.1 A resolution. The structure is of an alpha-beta fold and protein molecules form dimer. Based on the structural peculiarities, the part of small domain (residues 133 - 202) swings back while interacting with adenosyl ligand to make compact patch. The binding region of biotin carboxylase is much conserved in different bacteria species. In accordance with what was found earlier in adenine-binding region Glu201-Leu204 and Ile157-Lys159 Leu204 is substituted by Ile204, ribose-binding region is formed by His209, Gln233, His236 and Ile437 is changed to Thr437, and His438 to Asn438. Phosphate groups of the ligand interact with glycine-rich group (residues 162-168) together with Lys116, Lys159 and Gln237 which interacts with the third phosphate group of the ligand.  
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
    CA calcium ion crystallization
    CAC cacodylate ion crystallization
    AXP 4-acetamido-2,4-didexoy-d-glycero-beta-d-galacto-octopy ranosylphosphonic acid (an axial phosphonate) biological
    GOL glycerol
    FMT formic acid
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=89.83Å, b=100.17Å, c=148.70Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    63.03  
    Matthews coefficient
    3.33  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    44.92-2.25Å (2.33-2.25Å)  
    Rall(%)
    17.0  
    Rwork(%)
    16.8 (2350.0)  
    Rfree(%)
    22.0 (2890.0)  
    Num. observed reflections
    67052 (6247)  
    Num. Rfree reflections
    3399 (296)  
    Completeness(%)
    99.4 (99.0)  

    Model parameters

    Num Atoms
    7784  
    Num Waters
    633  
    Num Hetatoms
    79  
    Model mean isotropic B factor (Å2)
    28.890  
    RMSD bond length (Å)
    0.011  
    RMSD bond angle
    1.309°  
    RMSD dihedral angle
    17.182°
     
    Filename uploaded
    dep.pdb (uploaded on Sep 17, 2010 8:47 AM)  
    Inserted
    Sep 17, 2010