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Structure of IDP90525

1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961

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CSGID target
IDP90525 
PDB Id
3LDV (NCBI MMDB) 
Authors
Halavaty, A.S. Shuvalova, L. Minasov, G. Dubrovska, I. Winsor, J. Glass, E.M. Peterson, S.N. Anderson, W.F. Center for Structural Genomics of Infectious Diseases (CSGID)  
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jan 13, 2010 
Release Date
Jan 26, 2010 

Annotation

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Description
Orotidine 5′-monophosphate decarboxylase catalyses the decarboxylation of orotidine 5′-monophosphate to uridine 5′-monophosphate (UMP) without the aid of any metal ions or cofactors. This reaction is the last step in the de novo synthesis of pyrimidine nucleotides. We have determined an apo-structure of orotidine 5′-monophosphate decarboxylase from Vibrio cholerae. Two chains of the protein in the asymmetric unit form a closely bound homodimer. Each subunit of the dimer folds as an alpha/beta-barrel with eight central beta-strands flanked by eleven alpha helices. There is one active sites per subunit located at the C termini of the beta-strands of the barrel. Residues from both chains contribute to formation of each active site. A conserved unique motif Lys-Asp-Lys-Asp of the active site is present in the V. cholerae decarboxylase. Structures of binary complexes with UMP and known inhibitor 1-(5′-phospho-beta-D-ribofuranosyl)barbituric acid (BMP) can help to elucidate the mechanism of the reaction catalyzed by the protein.  
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
    MG unknown
    CL chloride ion

    Structure information

    View structure information | Edit structure information (upload a PDB file)

    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=47.30Å, b=94.67Å, c=99.18Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    38.46  
    Matthews coefficient
    2  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    30.00-1.77Å (1.82-1.77Å)  
    Rall(%)
    15.5  
    Rwork(%)
    15.4 (22.9)  
    Rfree(%)
    18.5 (26.2)  
    Num. observed reflections
    43729 (3076)  
    Num. Rfree reflections
    2186 (164)  
    Completeness(%)
    99.4 (95.8)  

    Model parameters

    Num Atoms
    3637  
    Num Waters
    593  
    Num Hetatoms
    608  
    Model mean isotropic B factor (Å2)
    29.090  
    RMSD bond length (Å)
    0.010  
    RMSD bond angle
    1.383°  
    Filename uploaded
    3LDV.pdb (uploaded on Sep 17, 2010 5:41 PM)  
    Inserted
    Jan 14, 2010