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The Open Protein Structure Annotation Network
PDB Keyword
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3i0z

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

    Title Crystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3i0z Target Id 391414
    Molecular Characteristics
    Source Streptococcus pneumoniae tigr4
    Alias Ids TPS20239,NP_344614.1, 3.40.50.10490, 336128 Molecular Weight 43104.85 Da.
    Residues 388 Isoelectric Point 4.89
    Sequence mlhytkedllelgaeittreiyqqpdvwreafefyqakreeiaaflqeiadkhdyikviltgagtsayv gdtllpyfkevyderkwnfnaiattdivanpatylkkdvatvlvsfarsgnspeslatvdlakslvdel yqvtitcaadgklalqahgddrnllllqpavsndagfamtssftsmmlttllvfdptefavkserfevv sslarkvldkaedvkelvdldfnrviylgagpffglaheaqlkileltagqvatmyespvgfrhgpksl indntvvlvfgtttdytrkydldlvrevagdqiarrvvllsdqafglenvkevalgcggvlndiyrvfp yivyaqlfalltslkvenkpdtpsptgtvnrvvqgviiheyqk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.178
    Matthews' coefficent 2.32 Rfactor 0.139
    Waters 825 Solvent Content 46.94

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3i0z

    Protein Summary

    Pfam:  this target belongs to SIS (PF01380) family, with two sugar isomerase domains on it.

     

    Gene NP_344614.1 encodes a protein with 388 residues from Streptococcus Pneumoniae, which is a Gram-positive, alpha-hemolytic diplococcus aerotolerant anaerobe and a member of the genus Streptococcus.  A significant human pathogenic bacterium, S. pneumoniae was recognized as a major cause of pneumonia in the late 19th century and is the subject of many humoral immunity studies.  The NCBI sequence alignment indicates that this protein contains SIS_GlmS_GlmD_1 and SIS_AgaS_like domains belonging to the SIS superfamily. The overall structure of this target contains two domains with almost identical architecture.  Each domain presents a three-layer αβα-sandwich architecture consisting of a five-strand parallel β-sheet flanked on each side by α-helices asymmetrically. Similar to its structural homologus(PDB: 1MOS, 1J5X) suggested by SSM and FFAS sever, Lys 250, Glu253 and His 271 are strictly conserved in the structure for the proposed glucosamine phosphate isomerization.  The conserved active site is Serine-riched for phosphate anchor.  Slightly different from it structural homolog 1MOS, Ser121 is mutated from Thr 504 in 1MOS.  A phosphate anion from protein preparation is modeled in the active site with unambiguous electron density support. A simple superposing/docking of 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE   based on the position of phosphate indicates that Arg 117 may also involve in the sugar-ring open step during the isomerization.  
    Crystal packing analysis using the EBI PISA web server shows that a dimer comprising two subunits of the asymmetric unit in the crystal structure may be a significant oligomerization state in solution. 

     

    391414_2.png

    Figure 1. The NP_344614.1 molecule contains two domains with identical

    fold: a three-layer αβα-sandwich.

     

     

    391414_1.png

    Figure 2. The biomolecule of NP_344614.1 is a tight dimer based on interface interaction.

     

     

    391414_4.png

    Figure 3. Protein NP_344614.1 (green) is structural homolog to 1MOS, 3CJ1 and

    1J5X with a conserved PO4 binding site.

     

     

     

     

     

     

     

    391414_3.png

    Figure 4. An AGP molecule is docked in the conserved active site via superposing the phosphate groups between AGP and phosphate anion in this target.  

     

    References,

    1.    Teplyakov, A.,  Obmolova, G.,  Badet-Denisot, M.A.,  Badet, B.   (1999) The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.  Protein Sci.   8: 596-602   
     
     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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