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3jzd

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

    Title Crystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3jzd Target Id 394332
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS25302,YP_298327.1, _0056.000797_ Molecular Weight 37143.13 Da.
    Residues 357 Isoelectric Point 6.07
    Sequence mkssqpfiyeahaarvvfgagsssqvaaeverlgakralvlctpnqqaeaeriadllgplsagvyagav mhvpiesardatarareagadcavavgggsttglgkaialetgmpivaipttyagsevtpvyglteagt krtgrdprvlprtviydpaltvglprglsvtsalnaiahaaeglyardanpvmslmaeegiralaagip avfndpadldarsqclygawlcgtvlggvgmalhhklchtlggsfnlphaethtivlphalaynaaavp eamarirratgageqsaaatlfdlaqrhgapvalrdigmreedldraadialaspywnprpierepira llqaayegvrpd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.10 Rfree 0.210
    Matthews' coefficent 3.35 Rfactor 0.174
    Waters 884 Solvent Content 63.33

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3jzd

    Protein Summary

    This protein is annotated as an iron-alcohol dehydrogenase belonging to the Pfam family PF00465 of Fe-ADH proteins.Pfam update: This protein is now in family PF00465.12 Fe-ADH CL0224.

    The JCSG has also solved the crystal structure of a related protein (~45% sequence identity). The TOPSAN annotation for that target can be found here.

    This protein structure was solved with 4 molecules in the asymmetric unit. Crystal packing analysis in conjunction with analytical SEC suggests that a dimer is the significant oligomeric form in solution:

    Fig1_dimer.png

    We did not find any iron in the structure, but found endogenous nicotinamide adenine dinucleotide (NAD) at the putative active sites of all 4 subunits in the asymmetric unit:

    Fig2_NAD.png

    The final modeled NAD is shown in the 2Fo-Fc (blue, 1.0 sigma) and Fo-Fc (green, 3.0sigma) electron density maps calculated without the NAD:

     NADomit.jpg

    Other similar proteins can be found via the BLAST and FFAS links above.

    A search for other proteins of similar structure using SSM indicated signficant similarities (Q-score > 0.6) to PDB accession ids 3bfj (1,3-Propanediol oxidoreductase, ~1.7A rmsd over ~330 residues, 31% sequence identity, Ref1), 1rrm (lactaldehyde reductase, ~1.7A rmsd over ~330 residues, 31% sequence identity), etc.

    Several histidine residues (H177, H242, H256, H260, H71, in blue) and a lysine (K105, green) around the NAD site could be functionally important.

    NAD_contacts.png

     

     

    References:

    1. J.Bacteriol. v191 pp. 1143-51, 2009
    1,3-Propanediol dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity.
    Marcal, D., Rego, A.T., Carrondo, M.A., Enguita, F.J. PUBMED.

    Ligand Summary

    Endogenous ligand NAD was modeled at the putative active sites.

    Reviews

    References

     

    No references found.

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