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The Open Protein Structure Annotation Network
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1vj0

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

    Title Crystal structure of Alcohol dehydrogenase (TM0436) from Thermotoga maritima at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 1vj0 Target Id 282309
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1204,TM0436, _0119.001924_, 84677 Molecular Weight 40555.61 Da.
    Residues 368 Isoelectric Point 6.04
    Sequence mmglkahamvlekfnqplvykefeisdiprgsilveilsagvcgsdvhmfrgedprvplpiilghegag rvvevngekrdlngellkpgdlivwnrgitcgecywckvskepylcpnrkvyginrgcseyphlrgcys shivldpetdvlkvsekddldvlamamcsgatayhafdeypesfagktvviqgagplglfgvviarslg aenviviagspnrlklaeeigadltlnrretsveerrkaimdithgrgadfileatgdsrallegsell rrggfysvagvavpqdpvpfkvyewlvlknatfkgiwvsdtshfvktvsitsrnyqllsklithrlplk eankalelmesrealkvilypeg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.00 Rfree 0.1939
    Matthews' coefficent 2.25 Rfactor 0.14539
    Waters 1192 Solvent Content 44.82

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vj0
    1. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
     
    2. Contribution of Electrostatic Interactions, Compactness and Quaternary Structure to Protein Thermostability: Lessons from Structural Genomics of Thermotoga
    M Robinson-Rechavi, A Alibs, A Godzik - Journal of molecular biology, 2006 - Elsevier
     
    3. Exploring structurally conserved solvent sites in protein families
    CA Bottoms, TA White, JJ Tanner - : Structure, Function, and , 2006 - Wiley Online Library
     
    4. Medium-and short-chain dehydrogenase/reductase gene and protein families
    H Eklund, S Ramaswamy - Cellular and molecular life sciences, 2008 - Springer
     
    5. Medium-and short-chain dehydrogenase/reductase gene and protein families
    DS Auld, T Bergman - Cellular and molecular life sciences, 2008 - Springer
     
    6. Protein structure alignment using elastic shape analysis
    W Liu, A Srivastava, J Zhang - Proceedings of the First ACM International , 2010 - dl.acm.org
     
    7. Biochemical and structural characterization of a ureidoglycine aminotransferase in the Klebsiella pneumoniae uric acid catabolic pathway
    JB French, SE Ealick - Biochemistry, 2010 - ACS Publications
     
    8. Bioinformatics of protein bound water
    CA Bottoms - 2005 - mospace.umsystem.edu
     

    Protein Summary

    The TM0436 gene of Thermotoga maritima encodes a zinc-containing alcohol dehydrogenase (ADH) comprising two domains, an N-terminal all-beta domain with a GroES-like fold (PF08240) and a C-terminal Rossmann fold (PF00107). Sequence, structure and genomic analyses indicate that TM0436 is a putative L-threonine 3-dehydrogenase (TDH) (EC 1.1.1.103), with a metabolic role in glycine oxidation and biosynthesis of vitamin B12 (Newman 1976).

    TM0436 forms a homotetramer and shows both sequence and structural similarity with other ADHs. The location of TM0436 in the pathway maps of the KEGG database indicates an involvement in glycine, serine and threonine metabolism. The closest structural neighbor of TM0436 is the TDH from Thermus thermophilus (PDB id: 2ejv) with a sequence identity of 29% and a structural superposition with an RMSD of 1.7 Å over 323 residues. The superposition of 2ejv with 1vj0 allowed for docking of the substrate NAD(H) along the highly conserved sequence motif GxGxxG (residues 191-196) (Fig.1).



    Figure 1. Docking of NAD(H), shown in red, onto TM0436. Surface representation of TM0436 (PDB id: 1vj0) is shown in green. The primary determinant of nicotinamide cofactor specificity (GxGxxG motif) is indicated in yellow and labeled.

    Sequence alignments show that residues involved in the coordination of the catalytic and structural zincs (Fig. 2) are highly conserved among ADHs. Removal of the structural zinc ions from the TDH of Pyrococcus horikoshii, another hyperthermophile, decreases the thermostability of the enzyme, suggesting that the coordination geometry of the zinc ions at this position contributes to the thermostability of the protein (Ishikawa 2007). Substrate specificity for TDH is thought to be derived from a salt-bridge in the vicinity of the active site, resulting in the catalytic zinc ion being less tightly bound in TDHs than in ADHs (Ishikawa 2007). The residues implicated in this bond (Glu66, Lys361 in TM0436) are conserved both in sequence and structure in TDHs, lending further support to the hypothesis that TM0436 acts as a TDH.



    Figure 2. Ribbon representation of zinc sites in TM0436. Zinc ions are shown in blue. Structural zincs at the dimer interface are coordinated by four cysteine residues (Cys 100, Cys 103, Cys 106 and Cys 115). The catalytic zinc is coordinated by Glu66, Cys43, His65 and Cys 166.

         

     

     

    Ligand Summary

    4 x NAD(H)
    8 x Zn (4 structural, 4 catalytic)
    4 x threonine (putative)

    References

    Reviews

    References

     

    No references found.

    Files (2)

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    183.78 kB22:01, 30 Jun 2008dweekesActions
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