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The Open Protein Structure Annotation Network
PDB Keyword
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1o4t

    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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1275,TM1287, 2.60.120.10, 84744, 89416
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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

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    (chain A, Z=16),
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    (chain A, Z=15), TM1010
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    (Z=14), TTHA0104
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    (Z=14),
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    (chain A, Z=12),
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    (chain A, Z=13),
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    (chain A, Z=12),
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    (chain A),
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    (chain A),
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    (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



    References

    Reviews

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