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1kq3

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

    Title Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc.Natl.Acad.Sci.USA 99 11664-11669 2002
    Site JCSG
    PDB Id 1kq3 Target Id 282296
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1203,TM0423, _0022.001675_, 84978 Molecular Weight 39689.39 Da.
    Residues 364 Isoelectric Point 5.17
    Sequence mitttifpgryvqgagainileeelsrfgerafvviddfvdknvlgenffssftkvrvnkqifggecsd eeierlsglveeetdvvvgigggktldtakavayklkkpvvivptiastdapcsalsviytpngefkry lflprnpdvvlvdteivakaparflvagmgdalatwfeaesckqkyapnmtgrlgsmtayalarlcyet lleygvlakrsveeksvtpalekiveantllsglgfesgglaaahaihngltvlenthkylhgekvaig vlaslfltdkprkmieevysfceevglpttlaeigldgvsdedlmkvaekacdknetihnepqpvtskd vffalkaadrygrmrknlt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.189
    Matthews' coefficent 2.30 Rfactor 0.173
    Waters 227 Solvent Content 46.59

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1kq3
    1. The Pfam protein families database
    RD Finn, J Mistry, J Tate, P Coggill, A Heger - Nucleic acids , 2010 - Oxford Univ Press
     
    2. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
    SA Lesley, P Kuhn, A Godzik - Proceedings of the , 2002 - National Acad Sciences
     
    3. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    4. Structural and functional characterization of bulges and other short intrahelical deformations
    JP Cartailler, H Luecke - Structure, 2004 - Elsevier
     
    5. Real-space protein-model completion: an inverse-kinematics approach
    H Van Den Bedem, I Lotan, JC Latombe - Section D: Biological , 2004 - scripts.iucr.org
     
    6. Faster data-collection strategies for structure determination using anomalous dispersion
    A Gonzalez - Acta Crystallographica Section D: Biological , 2003 - scripts.iucr.org
     
    7. 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
     
    8. Medium-and short-chain dehydrogenase/reductase gene and protein families
    DS Auld, T Bergman - Cellular and molecular life sciences, 2008 - Springer
     
    9. Optimizing data collection for structure determination
    A Gonzalez - Acta Crystallographica Section D: Biological , 2003 - scripts.iucr.org
     
    10. Computing protein structures from electron density maps: The missing fragment problem
    I Lotan, H Van Den Bedem, AM Deacon - Foundations of Robotics , 2005 - Springer
     
    11. Efficient recognition of protein fold at low sequence identity by conservative application of Psi_BLAST: application
    FJ Stevens, C Kuemmel, G Babnigg - Journal of Molecular , 2005 - Wiley Online Library
     
    12. Engineering of glycerol dehydrogenase for improved activity towards 1, 3-butanediol
    H Zhang, GT Lountos, CB Ching, R Jiang - Applied microbiology and , 2010 - Springer
     
    13. Zinc enzymes
    DS Auld - Encyclopedia of Inorganic and Bioinorganic , 2006 - Wiley Online Library
     
    14. Efficient recognition of protein fold at low sequence identity by conservative application of Psi_BLAST: validation
    FJ Stevens - Journal of Molecular Recognition, 2005 - Wiley Online Library
     
    15. Crystal structure of a zinc_containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 resolution
    LS Brinen, JM Canaves, X Dai - Proteins: Structure, , 2003 - Wiley Online Library
     
    16. Algorithms exploiting the chain structure of proteins
    I Lotan - 2004 - ai.stanford.edu
     
    17. The role of bias in crystallization conditions in automated microseeding
    FJ St John, B Feng, E Pozharski - Acta Crystallographica Section D: , 2008 - scripts.iucr.org
     
    18. Do Halide Motifs Stabilize Protein Architecture?
    P Zhou, F Tian, J Zou, Y Ren, X Liu - The Journal of Physical , 2010 - ACS Publications
     
    19. Automated protein model completion: an inverse kinematics approach
    H van den Bedem, I Lotan, JC Latombe - Acta Cryst , 2004 - www-cs-students.stanford.edu
     
    20. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     
    21. Crystallization and preliminary X-ray characterization of a glycerol dehydrogenase from the human pathogen Salmonella enterica serovar Typhimurium
    AT Goncalves, D Marcal, MA Carrondo - Section F: Structural , 2009 - scripts.iucr.org
     
    22. Modelling Protein Structure Using Discrete Backbone Torsion Angles
    P Smith - 2010 - unsworks.unsw.edu.au
     

    Protein Summary

    The TM0423 gene of Thermotoga maritima encodes a zinc-containing glycerol dehydrogenase (EC:1.1.1.6, PFAM:PF00465, COG:COG0371) that catalyzes the oxidation of glycerol to dihydroxyacetone with the simultaneous reduction of oxidized nicotinamide adenine dinucleatide (NAD+) to reduced nicotinamide adenine dinucleotide (NADH) (PubMed:12193646). 

    Enzyme similar to TM0423 is Fe-dependent and under anaerobic conditions is involved in dissimilation of glucose, and also has a protective role against oxidative stress in aerobic conditions (PMID:12783863).
    The discovery of a coenzyme B12 independent glycerol dehydratase (similar to TM0423), from Clostridium butyricum should significantly influence the development of an economical vitamin B12-free biological process for the production of 1,3-propanediol (1,3-PD) from renewable resources (PMID:12704244).

    Protein encoded by TM0423 has dehydroquinate synthase-like fold (SCOP sunid:56795) with 2 domains: 1st  - alpha/beta of a Rossmann-fold topology that binds NAD, and 2nd - multihelical array. This protein belongs to protein family of iron-containing alcohol dehydrogenases (SCOP sunid:69892). TM0423 has both sequence (FFAS03) and structural (FATCAT) similarity to several structures (i.e.: PDB:1jpuA, PDB:1ta9A, PDB:2bi4A, PDB:1vljA, PDB:1oj7A,  PDB:1dqsA, PDB:1xagA, and PDB:1ujnA).

    Ligand Summary



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