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The Open Protein Structure Annotation Network
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1vke

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

    Title Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution. To be published
    Site JCSG
    PDB Id 1vke Target Id 359877
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1442,TM1620 Molecular Weight 13364.78 Da.
    Residues 118 Isoelectric Point 6.94
    Sequence kkfvearrelnekvlsrgtlntkrffnldsavyrpgkldvktkelmglvastvlrcddciryhlvrcvq egasdeeifealdialvvggsiviphlrravgfleelremekngetisl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.56 Rfree 0.17834
    Matthews' coefficent 2.69 Rfactor 0.15816
    Waters 435 Solvent Content 53.93

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vke
    1. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
     
    2. Evolution of protein fold in the presence of functional constraints
    A Andreeva, AG Murzin - Current opinion in structural biology, 2006 - Elsevier
     
    3. Disulfide conformation and design at helix N_termini
    S Indu, ST Kumar, S Thakurela, M Gupta - Proteins: Structure, , 2010 - Wiley Online Library
     
    4. Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method
    S Ranganathan, D Izotov, E Kraka - Structure, Function, and , 2009 - Wiley Online Library
     
    5. Optimizations of protein force fields
    Y Sakae, Y Okamoto - Arxiv preprint arXiv:1208.6150, 2012 - arxiv.org
     
    6. Crystallization and preliminary X-ray crystallographic analysis of-carboxymucolactone decarboxylase from Sulfolobus solfataricus
    HY Lee, JK Yang - Section F: Structural Biology and Crystallization , 2009 - scripts.iucr.org
     
    7. Amino-acid-dependent main-chain torsion-energy terms for protein systems
    Y Sakae, Y Okamoto - Arxiv preprint arXiv:1206.3909, 2012 - arxiv.org
     

    Protein Summary

    TM1620 belongs (by sequence similarity) to carboxymuconolactone decarboxylase (CMD) family (Pfam02627), CMD, EC:4.1.1.44 is involved in protocatechuate catabolism. Some members of this family, such as Mycobacteriumtuberculosis alkylhydroperoxidase AhpD participate in bacterial antioxidant defense by regenerating its partner AhpC for further reduction of peroxides into alcohols. AhpD is responsible for M. tuberculosis resistance to isoniazid, a first-line antituberculous medication used in the prevention and treatment of tuberculosis.

    TM1620 has a AhpD-like fold consisting of two helical bundles, 3 helical on the N-terminal and 4-helical toward the C-terminal, connected by a V-shaped C-terminal helical hairpin. All of known proteins in this fold are likely to be related, as FFAS03 detects statistically significant (z-score between 60 and 25) similarity between them.

    JCSG recently solved several additional proteins from this family, (2pfx, 2oyo and 2ouw). Other members of this family were solved by other structural genomics centers.

    Interestingly, AhpD family is distantly related to human protein sestrin, p53 inducible protein involved in antioxidant defence (Budanov AV, Sablina AA, Feinstein E, Koonin EV, Chumakov PM.  Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science. 2004 Apr 23;304(5670):596-600. ) suggesting an ancient origin of DNA defence mechanisms in eukaryotic cells.

    Ligand Summary



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