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 Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 2ouw Target Id 370502
    Molecular Characteristics
    Source Rhodospirillum rubrum atcc 11170
    Alias Ids TPS1570,YP_425393.1, 91337 Molecular Weight 14724.06 Da.
    Residues 137 Isoelectric Point 5.26
    Sequence matvrllddaeistlpevkavfddiratrgsdfvnniwrglandpallkrtweqvktvmvgegaldplt remiylavstanscsycahshtaaarakgmtpaqhaevlaiiglaaqtnalvtamqipvdeaflvdgk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.95 Rfree 0.232
    Matthews' coefficent 2.04 Rfactor 0.195
    Waters 141 Solvent Content 39.80

    Ligand Information


    Google Scholar output for 2ouw
    1. Disulfide conformation and design at helix N_termini
    S Indu, ST Kumar, S Thakurela, M Gupta - Proteins: Structure, , 2010 - Wiley Online Library
    2. Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like structural family
    T Clarke, V Romanov, Y Chirgadze - BMC structural , 2011 - biomedcentral.com
    3. Intra-chain 3D Segment Swapping Spawns the Evolution of New Multidomain Protein Architectures
    A Szilgyi, Y Zhang, P Zvodszky - Journal of Molecular Biology, 2011 - Elsevier

    Protein Summary

    YP_425393.1 (UniProt:Q2RXN9_RHORT) belongs (by sequence similarity) to carboxymuconolactone decarboxylase (CMD) family (Pfam02627), CMD, EC: 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.

    YP_425393.1 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. 2ouw belongs to the AhpD-like superfamily, TTHA0727-like family.

    JCSG solved several proteins from the AhpD-like superfamily, starting with TM1620 (1vke), a member of the CMD-like family, and followed by members of the Atu0492-like family 2prr, 2pfx and 2oyo.

    Interestingly, AhpD family is distantly related to human protein sestrin, p53 inducible protein involved in antioxidant defence suggesting an ancient origin of DNA defence mechanisms in eukaryotic cells [Ref].

    Ligand Summary

    The following residues are within 4Å from the first UNL: Ile37, Val55, Tyr74, Tyr85, Cys86, Ser89, His90, Thr117, and Asn118.
    The following residues are within 4Å from the second UNL: Arg29, Asn35, Ile37, Trp38, Val55, Glu71, Tyr74, Tyr85, Cys86, Ser89, His90, Thr117, and Asn118.





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