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1o1x

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

    Title Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution. Proteins 56 171-175 2004
    Site JCSG
    PDB Id 1o1x Target Id 282947
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1258,TM1080, 84776 Molecular Weight 15866.34 Da.
    Residues 143 Isoelectric Point 6.42
    Sequence mkiaiasdhaafelkekvknyllgkgievedhgtyseesvdypdyakkvvqsilsneadfgillcgtgl gmsiaanryrgiraalclfpdmarlarshnnanilvlpgrligaelafwivdtflstpfdggrherrir kidev
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.138
    Matthews' coefficent 2.56 Rfactor 0.117
    Waters 212 Solvent Content 51.52

    Pathway

    Reactions found in Metabolic Reconstruction for TM1080

    Name: ribose-5-phosphate isomerase
    Metabolic Subsystem: Pentose Phosphate Pathway
    Reaction: : r5p <==> ru5p-D
    Classification: EC:5.3.1.6
     

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o1x
    1. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    3. 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
     
    4. Muscarinic receptors: a comparative analysis of structural features and binding modes through homology modelling and molecular docking
    A Pedretti, G Vistoli, C Marconi - Chemistry & , 2006 - Wiley Online Library
     
    5. Crystal structure of a ribose_5_phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 resolution
    Q Xu, R Schwarzenbacher, D McMullan - Proteins: Structure, , 2004 - Wiley Online Library
     
    6. Novel substrates of a ribose-5-phosphate isomerase from Clostridium thermocellum
    RY Yoon, SJ Yeom, HJ Kim, DK Oh - Journal of biotechnology, 2009 - Elsevier
     
    7. D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not
    AK Roos, S Mariano, E Kowalinski, L Salmon - Journal of molecular , 2008 - Elsevier
     
    8. Substrate specificity of ribose-5-phosphate isomerases from Clostridium difficile and Thermotoga maritima
    SJ Yeom, BN Kim, CS Park, DK Oh - Biotechnology letters, 2010 - Springer
     
    9. Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics
    J Jung, JK Kim, SJ Yeom, YJ Ahn, DK Oh - Applied microbiology and , 2011 - Springer
     
    10. Increased D-allose production by the R132E mutant of ribose-5-phosphate isomerase from Clostridium thermocellum
    SJ Yeom, ES Seo, YS Kim, DK Oh - Applied microbiology and , 2011 - Springer
     
    11. Structural and Functional Studies of Ribose-5-phosphate isomerase B
    AK Roos - 2007 - uu.diva-portal.org
     
    12. Structures of type B ribose 5_phosphate isomerase from Trypanosoma cruzi shed light on the determinants of sugar specificity in the structural family
    AL Stern, A Naworyta, JJ Cazzulo, SL Mowbray - FEBS Journal, 2011 - Wiley Online Library
     
    13. Of sequence and structure: Strategies of protein thermostability in evolutionary perspective
    IN Berezovsky, EI Shakhnovich - Arxiv preprint q-bio/0408007, 2004 - arxiv.org
     
    14. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     
    15. Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis
    TE Edwards, AB Abramov, ER Smith - BMC structural , 2011 - biomedcentral.com
     
    16. For Review Only
    A Naworyta, T de Chascoms, S Mowbray - FEBS Journal, 2011 - uu.diva-portal.org
     

    Protein Summary

    The TM1080 gene of Thermotoga maritima encodes the NP_228886 protein, a ribose-5-phosphate isomerase (RpiB; COG0698; pfam02502), that catalyzes the conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate.

    TM1080 has ribose/galactose isomerase RpiB/AlsB fold (SCOP sunid:89622) with 3 layers (a/b/a) sandwich, where parallel beta-sheet of 5 strands has a novel 21354 topology. The active site of TM1080 is likely to be located near the crevice formed at the C-terminal ends of strands beta-1, beta-3 and beta-5, which would place the active site at the dimer interface (PubMed:15162497). DALI provides the highest Z-score (27) with phosphate isomerases like PDB:3he8, PDB:2vvr, PDB:1nn4.

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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