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The Open Protein Structure Annotation Network
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3dde

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

    Title Crystal structure of Domain of Unknown Function with a Heme Oxygenase-like Fold (YP_564736.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3dde Target Id 370140
    Molecular Characteristics
    Source Shewanella denitrificans os217
    Alias Ids TPS6417,YP_564736.1, 291371 Molecular Weight 26917.21 Da.
    Residues 238 Isoelectric Point 5.21
    Sequence msiidltkleqkvatmwdsiltnspfihevldgkatkalyaiymtetyhytkhnaknqalvgimgkdlp gkylsfcfhhaheeaghelmalsdiasigfdredvlsskplpatetliaylywisatgnpvqrlgysyw aenvygyidpvlkaiqstldltpqsmkffiahskidakhaeevnemlhevcktqedvdsvvavmenslv ltarilddvwkeyqlfqsgasdryaflrdna
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.30 Rfree 0.253
    Matthews' coefficent 2.36 Rfactor 0.220
    Waters 74 Solvent Content 47.87

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dde
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    Gene Sden_3740 from Shewanella denitrificans os-217 encodes the YP_564736 protein that belongs to the TENA/THI-4/PQQC group ( Pfam  PF03070 ) (E-value: 1e-9).

    3dde is classified in the all alpha class, Heme oxygenase-like superfamily, TENA/THI-4 family from SCOP.

    3dde structure shows 2 molecules per asymmetric unit cell.


    The crystal packing analysis suggests that the biological unit should be a tetramer.
    There are a number of surface exposed histidine residues (on the surface of the predicted tetramer from the crystal structure) including His28,His78, His79, His81,His 170, His 177 (shown as red sticks in the figure below) which could be involved in protein function. Tyr119 (brown), Tyr 121 (cyan) and Trp122 (yellow) present at the oligomeric interface may participate in tetramer formation. Many of these residues are conserved in close sequence homologs as seen in a PSI-BLAST search.



    The most significantly similar proteins by FFAS are with PDB ids 1rcw (CT610, Ref1; Dali Z=22), 1otv (Coenzyme PQQ synthesis protein C, Ref2; Dali Z=20), 1z72 (a putative transcriptional regulator, Ref3; Dali Z=17) and 1udd (transcriptional regulator, Ref4; Dali Z=18). A search for structurally similar proteins by SSM also results in 1rcw and 1otw/1otv as the top two hits. Of these, 1rcw & 1z72 are dimers while 1otv & 1udd are tetramers. There is some difference in the relative orientation of the protomers forming the tetramer in this case.

    Pairwise alignment in FFAS shows that of the histidine residues mentioned and shown above,  His 170 (surface exposed in protomers B & D, in magenta and green next to each other) and His 177 (surface exposed in all 4 protomers) are analogous to His174/His 181 in 1rcw and His 175/Trp 183 in 1z72. In 1udd, the His 170 position is occupied by an aromatic residue (Tyr 166). As for the aromatic residues at the oligomeric interface (Y119, Y121 and W122, shown above) the similar proteins mostly have at least one aromatic residue in this region.

    Interestingly, the six residues that coordinate a di-iron binding site in the CT610 protein (CADD-Chlamydia protein associating with death domains, a redox enzyme that modulates host cell apoptosis, Ref1) Glu81, His88, Glu142, His174, Asp178 and His181 are strictly conserved in this protein as Glu83, His86, Glu140, His170, Asp174 and His181 (black sticks):



     

    Ligand Summary

    Reviews

    References

     

    No references found.

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