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Structure of IDP90546

1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168

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CSGID target
IDP90546 
PDB Id
3RU6 (NCBI MMDB) 
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
May 04, 2011 
Release Date
May 18, 2011 

Annotation

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Description
Orotidine monophosphate (OMP) decarboxylase catalyzes the final step in the de novo biosynthesis of uridine monophosphate. In most prokaryotes, OMP decarboxylase is a dimer of identical subunits, whereas in higher organisms, it is part of a bifunctional enzyme that also catalyzes the formation of OMP. The crystal structure of the apo-form Campylobacter jejuni orotidine 5'-monophosphate (OMP) decarboxylase was determined by molecular replacement and refined to an R-factor of 17.0% at 1.8 A resolution. There are two dimers in the asymmetric unit. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. Two iodide anions are bound at the active site in each of the four subunits. Surprisingly, Campylobacter jejuni and Bacillus subtilis OMP decarboxylases share only 31 % sequence identity, whereas they are very similar in structure with rmsd value of 1.7 A over 219 residues.  
Functional assignment
Lyase 
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
    IOD iodide ion crystallization
    CL chloride ion crystallization

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=44.60Å, b=108.31Å, c=97.71Å
    α=90.00, β=95.73, γ=90.00  
    Solvent content
     
    Matthews coefficient
     

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.12-1.80Å (1.85-1.80Å)  
    Rall(%)
    17.0  
    Rwork(%)
    16.8 (23.5)  
    Rfree(%)
    20.3 (24.5)  
    Num. observed reflections
    83983 (6125)  
    Num. Rfree reflections
    4199 (300)  
    Completeness(%)
    98.4 (97.5)  

    Model parameters

    Num Atoms
    7364  
    Num Waters
    549  
    Num Hetatoms
    591  
    Model mean isotropic B factor (Å2)
    32.770  
    RMSD bond length (Å)
    0.011  
    RMSD bond angle
    1.503°  
    Filename uploaded
    3RU6.pdb (uploaded on Jun 01, 2011 7:05 PM)  
    Inserted
    Jun 01, 2011