The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution. Proteins 56 392-395 2004
    Site JCSG
    PDB Id 1o4t Target Id 283151
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1275,TM1287,, 84744, 89416 Molecular Weight 13269.49 Da.
    Residues 121 Isoelectric Point 5.64
    Sequence mkegtgmvvrsseitperisnmrggkgevemahllskeamhnkarlfarmklppgssvglhkhegefei yyillgegvfhdngkdvpikagdvcftdsgeshsientgntdleflaviill
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.95 Rfree 0.217
    Matthews' coefficent 2.55 Rfactor 0.16
    Waters 198 Solvent Content 51.40

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    Ligand Information


    Google Scholar output for 1o4t
    1. The importance of alignment accuracy for molecular replacement
    R Schwarzenbacher, A Godzik - Section D: Biological , 2004 - scripts.iucr.org
    2. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
    3. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
    4. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
    R Schwarzenbacher, A Godzik - Section D: Biological , 2007 - scripts.iucr.org
    5. Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 resolution
    R Schwarzenbacher, F von Delft - Proteins: Structure, , 2004 - Wiley Online Library
    6. 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
    7. Crystal structure of a novel manganese_containing cupin (TM1459) from Thermotoga maritima at 1.65 resolution
    L Jaroszewski, R Schwarzenbacher - Proteins: Structure, , 2004 - Wiley Online Library
    8. Modeling the resting state of oxalate oxidase and oxalate decarboxylase enzymes
    M Scarpellini, J Gtjens, OJ Martin, JW Kampf - Inorganic , 2008 - ACS Publications
    9. Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157: H7
    LM van Staalduinen, CS Park, SJ Yeom - Journal of molecular , 2010 - Elsevier
    10. Crystal structure of XC5357 from Xanthomonas campestris: A putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure
    KH Chin, CC Chou, AHJ Wang - : Structure, Function, and , 2006 - Wiley Online Library
    11. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris
    HL Axelrod, P Kozbial, D McMullan - Section F: Structural , 2009 - scripts.iucr.org
    12. Of sequence and structure: Strategies of protein thermostability in evolutionary perspective
    IN Berezovsky, EI Shakhnovich - Arxiv preprint q-bio/0408007, 2004 - arxiv.org
    13. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu

    Protein Summary

    Gene TM1287 from Thermotoga maritima translates into the NP_229091 protein from the cupin-2 domain family (PF07883).

    TM1287 has a double-stranded beta-helix fold (SCOP sunid:51181), where one turn of helix is made by two pairs of antiparallel strands linked with short turns has the appearance of a  beta-sandwich of distinct architecture and jelly-roll topology. TM1287 belongs to RmlC-like cupins superfamily (SCOP sunid:51182), TM1287-like family. Similar structures according to DALI are: TM1459 protein PDB:1vj2 (chain A, Z=16), PDB:1v70 (chain A, Z=15), TM1010 PDB:2f4p (Z=14), TTHA0104 PDB:2dct (Z=14), PDB:2h0v (chain A, Z=12), PDB:1lr5 (chain A, Z=13), PDB:1yhf (chain A, Z=12), PDB:1rc6 (chain A), PDB:2f4p (chain A), PDB:1sef (chain A), PDB:2b8m (chain A), PDB:1x7n (chain A), PDB:1sfn (chain A), PDB:1j3p (chain A), PDB:1gqg (chain A), PDB:1sq4 (chain A), PDB:1fi2 (chain A), PDB:2fqp (chain A), and PDB:1j58 (chain A). 

    1o4t structure was crystallized in the presence of oxalate and manganese. This hypothetical oxalate decarboxylase reveals a bidentate oxalate coordination to the active site manganese ion that in turn chelates residues H61, H63, E68 and H102 (PubMed:15211523). Oxalate decarboxylases regulate oxalate levels in plants and microbes by a Mn2+/O2-dependent carbon-carbon bond cleavage that results in the conversion of oxalate to CO2 and formate.

    Ligand Summary





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