The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 1vqt Target Id 282207
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1200,TM0332, 282166 Molecular Weight 22807.49 Da.
    Residues 201 Isoelectric Point 6.97
    Sequence mtpvlsldmedpirfidengsfevvkvghnlaihgkkifdelakrnlkiildlkfcdipstversiksw dhpaiigftvhscagyesveralsatdkhvfvvvkltsmegsledymdrieklnklgcdfvlpgpwaka lrekikgkilvpgirmevkaddqkdvvtleemkgianfavlgreiylsenprekikrikemrl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.22088
    Matthews' coefficent 2.58 Rfactor 0.18139
    Waters 62 Solvent Content 52.04

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    Ligand Information


    Google Scholar output for 1vqt
    1. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
    R Schwarzenbacher, A Godzik - Section D: Biological , 2007 - scripts.iucr.org
    2. Structural basis for the decarboxylation of orotidine 5_-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase
    K Tokuoka, Y Kusakari, SR Krungkrai - Journal of , 2008 - Jpn Biochemical Soc
    3. Structure and Inhibition of Orotidine 5_-Monophosphate Decarboxylase from Plasmodium falciparum
    DB Langley, M Shojaei, C Chan, HC Lok - Biochemistry, 2008 - ACS Publications
    4. Protein structural classification and family identification by multifractal analysis and wavelet spectrum
    SM Zhu, ZG Yu, A Vo - Chinese Physics B, 2011 - iopscience.iop.org

    Protein Summary

    The TM0332 gene of Thermotoga maritima encodes an orotidine 5'-phosphate decarboxylase (OPDase) (PF00215, COG0284, EC The structure adopts a TIM barrel alpha/beta fold and is very similar to other bacterial OPDases including orthologs from Escherichia coli (PDB id: 1l2u, backbone rmsd 1.7 Å over 180 residues, 28% sequence identity), Bacillus subtilis (PDB id: 1dbt, backbone rmsd 1.9 Å over 185 residues, 26% sequence identity) and Geobacillus kaustophilus (PDB id: 2yyu, backbone rmsd 1.8 Å over 182 residues, 26% sequence identity). Further discussion of the structure, active site, catalytic mechanism and conformational changes induced by substrate binding can be found at Harris 2002.

    Ligand Summary





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