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3pi7

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

    Title Crystal structure of a putative NADPH:quinone reductase (mll3093) from Mesorhizobium loti at 1.71 A resolution. To be published
    Site JCSG
    PDB Id 3pi7 Target Id 393997
    Molecular Characteristics
    Source Mesorhizobium loti maff303099
    Alias Ids TPS25764,NP_104277.1, _0052.006031_, _0090.002341_ Molecular Weight 37831.76 Da.
    Residues 348 Isoelectric Point 6.87
    Sequence mspmtipsemkalllvgdgytktpsgsaleamepyleqgriavpapgpsqvlikvnlasinpsdvafik gqygqprvkgrpagfegvgtivaggdepyakslvgkrvafatglsnwgswaeyavaeaaaciplldtvr dedgaamivnpltaiamfdivkqegekafvmtagasqlckliiglakeegfrpivtvrrdeqiallkdi gaahvlnekapdfeatlrevmkaeqprifldavtgplasaifnampkrarwiiygrldpdatvirepgq lifqhkhiegfwlsewmrqfkerrgpaileaqkrfsdgrwstdvtavvplaeaiawvpaeltkpngkvfirp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.71 Rfree 0.2088
    Matthews' coefficent 2.05 Rfactor 0.1704
    Waters 299 Solvent Content 40.02

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     Gene mll3093 from Mesorhizobium loti encodes for a putative NADPH:quinone reductase (NP_104277.1, PFAM:PF08240 and PFAM:PF00107, COG:COG0604, CDD:176251) with many solved structures solved for these PFAM families.

     

    There are already 31 deposited homologs of this target in pdb, including PDB:3iup with highest similarity (26% sequence identity), which is the jcsg NADPH:quinone oxidoreductase structure (2.8Å rmsd, Z=28 by DALI alignment). Further high scoring DALI matches include PDB:1qor (Z=27, 2.5Å rmsd, 16% seq. id.), PDB:1yb5 (Z=27, 3.0Å rmsd, 18% seq. id.), PDB:3jyl (Z=26, 2.7Å rmsd, 18% seq. id.), altogether quinone oxidoreductases. Then there is a hit to PDB:2vcy (Z=26, 2.9Å rmsd, 23% seq. id.), TRANS-2-ENOYL THIOESTER REDUCTASE OF HUMAN FAS II. There is nothing new about this particular structure. The 2 domain dimeric enzyme has nothing bound in the pantetheine binding cleft near the active side, despite of the presence of the phosphate ions from the crystallization buffer. Picture below shows the  2 domain NP_104277.1 fold with overlapped ligands from the very conserved  known homologs.

     2wekOVERLAP.jpg

     

     

     

     

     

    Among the most conserved residues in Dali overlap of the structures with the highest RMSD are E85,D64,N61,L326, all mostly concentrated around the beta-barrel domain of the fold. The other part of the molecule, i.e. the beta-sheet wall, participates in the dimerization process (according to PISA prediction and 3D comparison with other dimers of this family), in which 2 beta-sheets each with 6 strands align with each other forming a ~45A long twisted “tube” around which 2 nucleotides belonging to each monomer are wrapped(picture below). The possible substrates are bound just around the dimer-interface on the border of that beta-sheet tube. All ligands bound to NP_104277.1 are concentrated more around the higher conserved part of the molecule, facing the outer part of the dimer, not participating in the nucleotide binding groove. Overall the whole dimer comprises 3 twisted beta-sheet “tubes” rotated to each other by ~90deg starting from one 'edge' of the dimer.

     DIMER-tube1.jpg

     

     

     

     

     

    Arg and LYS cluster distributed across the 2 domains cover in 3d in average similar areas when compared with the 2 mentioned pdb's, which leads to a rough speculation, that similar (charge conservation) residues for this protein are both in humans as well as in the symbotic nitrogen fixing bacteria, from which the NP_104277.1  target originates.

    Refinement notes:

    Section 315-321 completely disordered, possible multiple conformations of the whole chain. Trials with Buster, improved the final fit, but the uncertainty is still there. Cocrystallization with NADPH could improve that section according to the literature[1].

    [Ref]

    Ligand Summary

    Reviews

    References

     

    1. (No Results)

       


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    Files (3)

    FileSizeDateAttached by 
     2wekOVERLAP.jpg
    MH10766A with ligands and superposed substrate from a homolog
    363.77 kB02:20, 16 Apr 2010cbtrameActions
     DIMER-tube1.jpg
    Dimer arrangement with supersposed nucleotide in one monomer from homolog structure
    238.25 kB02:25, 16 Apr 2010cbtrameActions
     ELECTRO-DIMER.jpg
    Electrostatics of the dimer interface of MH10766A
    364.2 kB02:22, 16 Apr 2010cbtrameActions
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