.
The Open Protein Structure Annotation Network
PDB Keyword
.

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
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS1203,TM0423, _0022.001675_, 84978
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 1
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.30 Rfactor 0.173
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 46.59

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Access denied for user 'root'@'localhost' (using password: YES) (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    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
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    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



    References

    Reviews

    References

     

    No references found.

    Tag page

    Files (0)

     
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch