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The Open Protein Structure Annotation Network
PDB Keyword
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3fxa

    Title Crystal structure of putative sugar-phosphate isomerase (YP_013136.1) from Listeria monocytogenes 4b F2365 at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 3fxa Target Id 390915
    Molecular Characteristics
    Source Listeria monocytogenes str. 4b f2365
    Alias Ids TPS20172,YP_013136.1, 3.40.50.10490, 85273 Molecular Weight 21314.51 Da.
    Residues 200 Isoelectric Point 5.38
    Sequence mdkqaildnihqtwqeeanaisrlpevtseealvktvekiaectgkivvagcgtsgvaakklvhsfnci erpavfltpsdavhgtlgvlqkedililiskggntgellnlipacktkgstligvtenpdsviakeadi ffpvsvskepdpfnmlatastmaviasfdavivclmtymnytkeqfsvihpggavgnkllnk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.60 Rfree 0.157
    Matthews' coefficent 2.22 Rfactor 0.133
    Waters 443 Solvent Content 44.54

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fxa
    1. Probing the active site of the sugar isomerase domain from E. coli arabinose_5_phosphate isomerase via X_ray crystallography
    LJ Gourlay, S Sommaruga, M Nardini - Protein , 2010 - Wiley Online Library
     
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    3. A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073
    JA Mosberg, A Yep, TC Meredith, S Smith - Journal of , 2011 - Am Soc Microbiol
     

    Protein Summary

    Gene LMOf2365_0531 from Listeria monocytogenes 4b f2365 encodes the YP_013136 whose residues 39-172 contain a SIS  domain (PF01380 ). SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway.

     Pre-SCOP classifies 3fxa in the alpha/beta class, SIS domain superfamily, mono SIS domain family.

    The 3fxa monomer structure is shown below with the SIS domain highlighted.

    SIS_39_172.png

    Structures similar to 3fxa, see the table below, also lend evidence to this protein being a sugar isomerase.

    DALI Structural Similarity Search using 3fxa as Query
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3etn 25.5 1.5 184 192 35 PUTATIVE PHOSPHOSUGAR ISOMERASE INVOLVED IN
    2 1vim 21.8 2.3 177 190 21 HYPOTHETICAL PROTEIN AF1796
    3 1m3s 21.1 2.7 173 181 21 HYPOTHETICAL PROTEIN YCKF
    4 1jeo 20.9 2.2 167 177 21 HYPOTHETICAL PROTEIN MJ1247
    5 1viv 20.7 2.5 172 184 22 HYPOTHETICAL PROTEIN YCKF
    6 2i2w 18.6 2.5 163 178 21 PHOSPHOHEPTOSE ISOMERASE
    7 2v4m 18.5 3.7 173 350 18 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    8 2i22 18.5 2.5 163 178 21 PHOSPHOHEPTOSE ISOMERASE
    9 2yva 18.4 2.3 163 193 17 DNAA INITIATOR-ASSOCIATING PROTEIN DIAA
    10 1x94 18.4 2.4 162 176 22 PUTATIVE PHOSPHOHEPTOSE ISOMERASE

     

    A superposition of the above structures highlight the structural similarity.

    MG0829T_all.png

    Color code: 3fxa (green), 1jeo (cyan), 1m3s (lightmagenta), 1vim (yellow), 1viv (salmon), 1x94 (lightgrey), 2i22 (slate), 2i2w (orange), 2yva (deepteal), 3etn (hotpink).

     

    The protein assembles as a dimer of dimers in the crystal structure of 3fxa.

    MG0829T_tetramer.pngMG0829T_dimer.png

    Tetramer                                                                            Dimer

     

    There is some unmodeled density (Fo-Fc difference density) near residue His188 from chain D shown below. This region is not the putative active site of the molecule; rather, it is at the end of the chain D and adjacent to the chain C of the protein.

    D188.png

    Refinement Notes:

    The diffraction data is twinned with the operator "-K, -H, -L" with the twin fraction refined to 0.439.

     

    Literature references
    1. Bateman A; , Trends Biochem Sci 1999;24:94-95.: The SIS domain: a phosphosugar-binding domain. PUBMED:10203754

    2. Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B, Polikarpov I; , Structure 1998;6:1047-1055.: Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. PUBMED:9739095

    Ligand Summary

    Reviews

    References

     

    No references found.

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