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

    Title Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 1o5k Target Id 283378
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1296,TM1521, 84792, 89431 Molecular Weight 32388.59 Da.
    Residues 294 Isoelectric Point 5.91
    Sequence mfrgvgtaivtpfkngeldlesyerlvryqlengvnalivlgttgesptvnedereklvsrtleivdgk ipvivgagtnstektlklvkqaeklgangvlvvtpyynkptqeglyqhykyisertdlgivvynvpgrt gvnvlpetaariaadlknvvgikeanpdidqidrtvsltkqarsdfmvwsgnddrtfyllcaggdgvis vvsnvapkqmvelcaeyfsgnleksrevhrklrplmkalfvetnpipvkaalnlmgfienelrlplvpa sektvellrnvlkesgll
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.18593
    Matthews' coefficent 2.12 Rfactor 0.13941
    Waters 508 Solvent Content 41.42

    Pathway

    Reactions found in Metabolic Reconstruction for TM1521

    Name: dihydrodipicolinate synthase
    Metabolic Subsystem: Lysine Biosynthesis
    Reaction: : aspsa + pyr --> 23dhdp + h + h2o
    Classification: EC:4.2.1.52
     

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o5k
    1. The importance of alignment accuracy for molecular replacement
    R Schwarzenbacher, A Godzik - Section D: Biological , 2004 - scripts.iucr.org
     
    2. The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological
    RCJ Dobson, MDW Griffin, GB Jameson - Section D: Biological , 2005 - scripts.iucr.org
     
    3. Dihydrodipicolinate synthase from Thermotoga maritima
    FG Pearce, MA Perugini, HJ Mckerchar - Biochemical , 2006 - ncbi.nlm.nih.gov
     
    4. Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis
    G Kefala, G Evans, M Griffin, S Devenish, F Pearce - Biochem. J, 2008 - biochemj.org
     
    5. Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 resolution
    E Blagova, V Levdikov, N Milioti - Proteins: Structure, , 2006 - Wiley Online Library
     
    6. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
     
    7. Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase
    TS Girish, E Sharma, B Gopal - FEBS letters, 2008 - Elsevier
     
    8. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    9. Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein
    EA Rice, GA Bannon, KC Glenn, SS Jeong - Archives of biochemistry , 2008 - Elsevier
     
    10. Conserved main_chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase
    RCJ Dobson, MDW Griffin, SRA Devenish - Protein , 2008 - Wiley Online Library
     
    11. High throughput processing of the structural information in the protein data bank
    Z Szabadka, V Grolmusz - Journal of Molecular Graphics and Modelling, 2007 - Elsevier
     
    12. The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum
    RCJ Dobson, SC Atkinson, MA Gorman - Section F: Structural , 2008 - scripts.iucr.org
     
    13. Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii
    B Padmanabhan, RW Strange, SV Antonyuk - Section F: Structural , 2009 - scripts.iucr.org
     
    14. Characterisation of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization
    FG Pearce, RCJ Dobson, GB Jameson - et Biophysica Acta (BBA , 2011 - Elsevier
     
    15. Crystal structure of YagE, a putative DHDPS_like protein from Escherichia coli K12
    S Manicka, Y Peleg, T Unger, S Albeck - Proteins: Structure, , 2008 - Wiley Online Library
     
    16. Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis
    V Bhaskar, M Kumar, S Manicka - Proteins: Structure, , 2011 - Wiley Online Library
     
    17. Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism
    N Shimada, B Mikami, S Watanabe - Section F: Structural , 2007 - scripts.iucr.org
     
    18. Structural investigation of MosA
    KH Nienaber - 2008 - library.usask.ca
     

    Protein Summary

    The gene TM1521 from Thermotoga maritima encodes dihydrodipicolinate synthase, a DHDPS enzyme superfamily PF00701 COG0329.  DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.  The other name of the enzyme is N-acetylneuraminate lyase.  DHDPS is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta-semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a conserved lysine residue [Ref]. The functional enzyme is a homotetramer consisting of a dimer of dimers. The activity of DHDPS is allosterically regulated by the feedback inhibitor (S)-lysine.  The structure of E.coli homologue and its multiple mutant forms have been previously solved 1S5W, 2A6N.

    Ligand Summary



    References

    Reviews

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