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1o2d

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

    Title Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution. Proteins 54 174-177 2004
    Site JCSG
    PDB Id 1o2d Target Id 375013
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1639,TM0920, 84902 Molecular Weight 39940.89 Da.
    Residues 359 Isoelectric Point 5.79
    Sequence mwefymptdvffgekilekrgniidllgkralvvtgkssskkngslddlkklldeteisyeifdeveen psfdnvmkaveryrndsfdfvvglgggspmdfakavavllkekdlsvedlydrekvkhwlpvveiptta gtgsevtpysiltdpegnkrgctlmfpvyafldprytysmsdeltlstgvdalshavegylsrkstpps dalaieamkiihrnlpkaiegnrearkkmfvasclagmviaqtgttlahalgyplttekgikhgkatgm vlpfvmevmkeeipekvdtvnhifggsllkflkelglyekvavsseelekwvekgsrakhlkntpgtft pekirniyrealgv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.30 Rfree 0.17
    Matthews' coefficent 1.92 Rfactor 0.137
    Waters 892 Solvent Content 35.36

    Pathway

    Reactions found in Metabolic Reconstruction for TM0920

    Name: alcohol dehydrogenase (glycerol)
    Genes involved in rxn:TM0920 TM0111
    Metabolic Subsystem: Alternate Carbon Metabolism
    Reaction: : glyald + h + nadh <==> glyc + nad
    Classification: EC:1.1.1.1
     
    Name: acetaldehyde dehydrogenase (acetylating)
    Genes involved in rxn:TM0920 TM0111
    Metabolic Subsystem: Pyruvate Met
    Reaction: : acald + coa + nad --> accoa + h + nadh
    Classification: EC:1.2.1.10
     

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o2d
    1. The importance of alignment accuracy for molecular replacement
    R Schwarzenbacher, A Godzik - Section D: Biological , 2004 - scripts.iucr.org
     
    2. Structural analysis of a set of proteins resulting from a bacterial genomics project
    J Badger, JM Sauder, JM Adams - Proteins: Structure, , 2005 - Wiley Online Library
     
    3. Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics
    W Shi, C Zhan, A Ignatov, BA Manjasetty, N Marinkovic - Structure, 2005 - Elsevier
     
    4. 3D-QSAR study for DNA cleavage proteins with a potential anti-tumor ATCUN-like motif
    H Gonzlez-Daz, Snchez-Gonzlez - Journal of inorganic , 2006 - Elsevier
     
    5. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    6. Crystal Structure of E. coli Alcohol Dehydrogenase YqhD: Evidence of a Covalently Modified NADP Coenzyme
    G Sulzenbacher, K Alvarez - Journal of molecular , 2004 - Elsevier
     
    7. Modelling bound ligands in protein crystal structures
    PH Zwart, GG Langer, VS Lamzin - Acta Crystallographica Section D: , 2004 - scripts.iucr.org
     
    8. Crystal structure of an iron-dependent group III dehydrogenase that interconverts L-lactaldehyde and L-1, 2-propanediol in Escherichia coli
    C Montella, L Bellsolell, R Prez-Luque - Journal of , 2005 - Am Soc Microbiol
     
    9. Crystal structure of an iron_containing 1, 3_propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 resolution
    R Schwarzenbacher, F von Delft - Proteins: Structure, , 2004 - Wiley Online Library
     
    10. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
    R Schwarzenbacher, A Godzik - Section D: Biological , 2007 - scripts.iucr.org
     
    11. 1, 3-propanediol dehydrogenase from Klebsiella pneumoniae: decameric quaternary structure and possible subunit cooperativity
    D Maral, AT Rgo, MA Carrondo - Journal of , 2009 - Am Soc Microbiol
     
    12. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum
    SD Brown, AM Guss, TV Karpinets - Proceedings of the , 2011 - National Acad Sciences
     
    13. Quantum Chemical Investigations on Intraresidue Carbonyl_ Carbonyl Contacts in Aspartates of High-Resolution Protein Structures
    TK Pal, R Sankararamakrishnan - The Journal of Physical , 2009 - ACS Publications
     
    14. Investigating diproline segments in proteins: Occurrences, conformation and classification
    I Saha, N Shamala - Biopolymers, 2012 - Wiley Online Library
     
    15. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     
    16. Expression, purification and X-ray analysis of 1, 3-propanediol dehydrogenase (Aq_1145) from Aquifex aeolicus VF5
    J Jeyakanthan, S Thamotharan, S Panjikar - Section F: Structural , 2010 - scripts.iucr.org
     
    17. Stereochemistry of hydride transfer by group III alcohol dehydrogenases involved in phosphonate biosynthesis
    SC Peck, SY Kim, BS Evans, WA van der Donk - MedChemComm, 2012 - pubs.rsc.org
     
    18. Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII
    K Poleszak, KH Kaminska - Nucleic Acids , 2012 - Oxford Univ Press
     
    19. TRIAL: A Tool for Finding Distant Structural Similarities
    J Venkateswaran, B Song, T Kahveci - /ACM Transactions on, 2011 - ieeexplore.ieee.org
     
    20. Cofactor_binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space
    B Stegemann, G Klebe - Proteins: Structure, Function, and , 2012 - Wiley Online Library
     

    Protein Summary

    The gene  TM0920 from Thermotoga maritima encodes an iron-containing 1,3-propanediol dehydrogenase, a member of alcohol dehydrogenases family PF00465. The enzyme belongs to the class of multi-domain alpha and beta (a+b) proteins and adopts  dehydroquinate synthase-like fold type with well-defined Rossmann-like domain  SCOP56795.  1,3- propanediol dehydrogenase catalyzes the oxidation of propane-1,3-diol to 3-hydroxypropanal with the simultaneous reduction of NADP to NADPH.  Another four alcohol dehydrogenase paralogues of TM0920 have been identified in the Thermotoga proteome (TM0111, TM0285, TM0423, and TM0820) [Ref].  Alcohol dehydrogenases are a group of oxidoreductases that catalyze the interconversion of alcohols and the corresponding aldehyde or ketone.  Many of enzymes from this family are used  in the pharmaceutical industry to catalyze the synthesis of chiral compounds [Ref].

    Ligand Summary


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