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2iiz

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

    Title Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69 234-243 2007
    Site JCSG
    PDB Id 2iiz Target Id 360890
    Related PDB Ids 2hag 
    Molecular Characteristics
    Source Shewanella oneidensis mr-1
    Alias Ids TPS1456,NP_716371.1, PF04261, 90484 Molecular Weight 35758.36 Da.
    Residues 311 Isoelectric Point 5.05
    Sequence mdiqnmpreqlgvcaegnlhsvylmfnandnvesqlrpcianvaqyiyeltdqysdsafngfvaigany wdslypesrpemlkpfpamqegnreapaieydlfvhlrcdrydilhlvaneisqmfedlvelveeergf rfmdsrdltgfvdgtenpkgrhrqevalvgsedpefkggsyihvqkyahnlskwhrlplkkqediigrt kqdnieyesedkpltshikrvnlkdengksieilrqsmpygslkeqglmfistcrtpdhfekmlhsmvf gdgagnhdhlmhftsaltgssffapsldflmqfdn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.266
    Matthews' coefficent 3.58 Rfactor 0.205
    Waters 112 Solvent Content 65.41

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2iiz
    1. DyP-type peroxidases comprise a novel heme peroxidase family
    Y Sugano - Cellular and molecular life sciences, 2009 - Springer
     
    2. Identification and structural characterization of heme binding in a novel dye_decolorizing peroxidase, TyrA
    C Zubieta, R Joseph, S Sri Krishna - Proteins: Structure, , 2007 - Wiley Online Library
     
    3. Crystal structures of two novel dye_decolorizing peroxidases reveal a __barrel fold with a conserved heme_binding motif
    C Zubieta, S Krishna, M Kapoor - Proteins: Structure, , 2007 - Wiley Online Library
     
    4. Heme proteinsdiversity in structural characteristics, function, and folding
    LJ Smith, A Kahraman - : Structure, Function, and , 2010 - Wiley Online Library
     
    5. Characterization of DyP Peroxidases from Rhodococcus jostii RHA1
    JN Roberts, R Singh, JC Grigg, MEP Murphy - Biochemistry, 2011 - ACS Publications
     
    6. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     
    7. The catalytic mechanism of dye_decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue
    T Yoshida, H Tsuge, H Konno, T Hisabori - FEBS , 2011 - Wiley Online Library
     
    8. 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
     
    9. Identification and Molecular Characterization of a Novel DyP-Type Peroxidase from Pseudomonas aeruginosa PKE117
    J Li, C Liu, BZ Li, HL Yuan, JS Yang - Applied biochemistry and , 2012 - Springer
     

    Protein Summary

    The gene SO_0740 from Shewanella oneidensis encodes a melanin biosynthesis protein TyrA belonging to the dye-decolorizing peroxidase (Dyp)-type peroxidase family PF04261.  TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold SCOP143265. Both domains contribute to the heme-binding site.  The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris, demonstrates conservation of this novel heme conformation, as well as residues important for heme binding [Ref].

    Ligand Summary


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