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1zh8

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

    Title Crystal structure of Oxidoreductase (TM0312) from Thermotoga maritima at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 1zh8 Target Id 282188
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1199,TM0312, 84870 Molecular Weight 36537.08 Da.
    Residues 328 Isoelectric Point 5.69
    Sequence mkplrkirlgivgcgiaarelhlpalknlshlfeitavtsrtrshaeefakmvgnpavfdsyeellesg lvdavdltlpvelnlpfiekalrkgvhvicekpistdvetgkkvvelseksektvyiaenfrhvpafwk akelvesgaigdpvfmnwqiwvgmdennkyvhtdwrkkpkhvggflsdggvhhaaamrlilgeiewisa vakdlspllggmdflssifefengtvgnytisyslkgnerfeitgtkgkisiswdkivlneeemkvpqe nsyqkefedfyqvvaegkpndlgspvqalkdlafieacvrsagnkvfvssll
      BLAST   FFAS

    Structure Determination
    Method Chains
    Resolution (Å) Rfree 0.237
    Matthews' coefficent 2.68 Rfactor 0.194
    Waters Solvent Content 53.69

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1zh8
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions
    A Banerji, I Ghosh - PloS one, 2009 - dx.plos.org
     
    3. Structure of monkey dimeric dihydrodiol dehydrogenase in complex with isoascorbic acid
    V Carbone, R Sumii, S Ishikura, Y Asada - Section D: Biological , 2008 - scripts.iucr.org
     
    4. Re-Annotation of Two Hyperthermophilic Archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638
    J Gao, J Wang - Current microbiology, 2012 - Springer
     
    5. How do thermophilic proteins resist aggregation?
    AM Thangakani, S Kumar - Proteins: Structure, , 2011 - Wiley Online Library
     
    6. Structural and functional features of dimeric dihydrodiol dehydrogenase
    V Carbone, A Hara, O El-Kabbani - Cellular and Molecular Life Sciences, 2008 - Springer
     
    7. Analysis of the GAL3 protein, a key component of the GAL gene transcription switch in Saccharomyces cerevisiae
    CQ Diep - 2006 - books.google.com
     

    Protein Summary

    The TM0312 gene from Thermotoga maritima encodes a putative NADPH-dependent oxidoreductase (PF01408, COG0673). The two-domain structure displays a Rossmann fold at the N-terminus and a glyceraldehyde-3-phosphate-like C-terminal domain. A GxGxxA motif, postulated as a consensus sequence for NADP(H)-binding proteins (Hanukoglu 1989) is located between the first strand and first helix of the Rossmann fold (residues 13-18) and is involved in creating a binding pocket for the NADP ligand.

     

    TM0312 displays strong structural similarity with another putative NADPH-dependent oxidoreductase from Desulfitoibacterium hafniense DCB-2 (PDB:3db2, see topsan page, main-chain rmsd of 1.7 Å over 301 residues and a sequence identity of 20%) and the 1,5-anhydro-D-fructose reductase (AFR) from Sinorhizobium morelense S-30 (PDB id: 2glx, main-chain rmsd of 1.8 Å over 305 residues and a sequence identity of 23%). Amino acid replacements in the N-terminal domain of AFR (S10G, A13G, and S33D) have shown that Ala13 (Ala18 in TM0312) is crucial for the discrimination between NADPH and NADH with the A13G variant exhibiting dual cosubstrate specificity (Dambe 2006). Site-directed mutagenesis in the C-terminal domain of AFT have shown that Lys96, Asp176 and His180 (corresponding to TM0312 residues Lys101, Asp186 and His190) are most likely involved in substrate binding and catalysis, as substitution of any of these residues resulted in a significant decrease in kcat for 1,5-anhydro-D-fructose (1,5-AF) (Dambe 2006).

     

    Given the overall structural similarity with AFR as well as conservation of catalytic site residues, TM0312 and 3db2 are likely implicated in the 1,5-AF pathway.

     

    Ligand Summary



    References

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