The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of putative ribose 5-phosphate isomerase (YP_001165900.1) from Novosphingobium aromaticivorans DSM 12444 at 1.81 A resolution. To be published
    Site JCSG
    PDB Id 3c5y Target Id 379606
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS1745,YP_001165900.1, 86622 Molecular Weight 22985.17 Da.
    Residues 212 Isoelectric Point 5.25
    Sequence mkialiiensqaaknavvhealttvaeplghkvfnygmytaedkasltyvmngllagillnsgaadfvv tgcgtgmgsmlaanampgvfcglvidptdaflfgqindgnaismpyskgfgwaaelnlqdvyrklfdge rglgypreraeimrknrgilrelkdascrdmltvlktvdqdllraaiagekfaelfypnckddaianyl rslda
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 16
    Resolution (Å) 1.81 Rfree 0.220
    Matthews' coefficent 2.31 Rfactor 0.170
    Waters 2665 Solvent Content 46.74

    Ligand Information


    Google Scholar output for 3c5y
    1. The translation regulatory subunit eIF3f controls the kinase-dependent mTOR signaling required for muscle differentiation and hypertrophy in mouse
    A Csibi, K Cornille, MP Leibovitch, A Poupon - PloS one, 2010 - dx.plos.org
    2. 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
    3. 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
    4. For Review Only
    A Naworyta, T de Chascoms, S Mowbray - FEBS Journal, 2011 - uu.diva-portal.org

    Protein Summary

    Gene Saro_3514 from Novosphingobium aromaticivorans dsm 12444 encodes the YP_001165900 protein that belongs to Ribose/Galactose Isomerase  group (PF02502). This family of proteins contains the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB).

    SCOP classifies 3c5y in the alpha/beta class, ribose/galactose isomerase RpiB/AlsB (super)family. 3c5y fold consists of a sheet flanked by several helices. According to DALI, there are several structures with significant similarity to 3c5y, all ribose phosphate isomerases: PDB:2PPW (Z-scr=34), PDB:3HEE (Z-scr=17), PDB:2VVR (Z-scr=17), PDB:1O1X (Z-scr=17), PDB:1NN4 (Z-scr=16), PDB:2BET (Z-scr=16).

    Ligand Summary

    Nitrate and Ethylene glycol from the crystallization/cryo conditions.





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