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3kws

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

    Title Crystal structure of Putative sugar isomerase (YP_001305149.1) from Parabacteroides distasonis ATCC 8503 at 1.68 A resolution. To be published
    Site JCSG
    PDB Id 3kws Target Id 396647
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS27984,YP_001305149.1, 327043 Molecular Weight 31130.74 Da.
    Residues 286 Isoelectric Point 5.51
    Sequence scsskpantakgekgsdktgkdlelklsfqegiapgeslnekldfmeklgvvgfepgggglagrvneik qalngrnikvsaicagfkgfilstdpairkecmdtmkeiiaaagelgstgviivpafngqvpalphtme trdflceqfnemgtfaaqhgtsvifeplnrkecfylrqvadaaslcrdinnpgvrcmgdfwhmtweets dmgafisggeylqhvhvasrkrrsmpgedgdadnyingfkglkmigynnyvsfecgcqgdrnvvvpaav kllreqweqa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.68 Rfree 0.182
    Matthews' coefficent 2.47 Rfactor 0.150
    Waters 820 Solvent Content 50.14

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3kws

    Protein Summary

    Pfam Update: This protein is now in family PF01261.17 AP_endonuc_2 CL0036 along with other structures.

     

    Target ID 396647 belongs to theAP_endonuc_2 (PF01261) Pfam A family. The structural basis for this Pfam class has been extensively investigated, with 159 structures deposited for the family in the PDB.

     

    monomer.png

     

    Shown below is a ribbon representation of the structure color-coded with the N-terminus in blue and the C-terminus in red. The structure was determined to a resolution of 1.68 Angstroms using three wavelength Se-multiwavelength anomalous dispersion. The structure of target ID 396647 is similar to those belonging to the Xylose isomerase-like SCOP superfamily. with a TIM beta/alpha barrel fold.

    Analytical size exclusion chromatography provide supporting evidence that a dimer is a significant oligomerization state in solution. Shown below is a ribbons representation of the dimer discerned from the crystal packing.

    dimer.png

     A DALI search using the refined coordinates of target ID 396647 shows that this target shows structural similarity to those in the table below.

    PDB ID Z-Score rmsd (Ang) Lalign nres %seq id Description
    2zvr 29.0 2.1 248 262 27 D-Tagatose 3-epimerase related protein from Thermotoga maritima
    2qum 28.1 2.3 251 290 20 D-tagatose 3-epimerase from Pseudomonas cichorii with D-tagatose
    2hk0 27.8 2.4 250 289 20 D-psicose 3-epimerase (DPEASE) in the absence of substrate
    3cqj 25.8 2.8 253 275 17 L-xylulose-5-phosphate-3-epimerase ULAE (form B) in complex with Zn2+
    1k77 25.6 2.9 246 260 14 Hypothetical protein YGBM from E. coli.
    2qw5 24.8 2.6 254 327 13 Putative Sugar Phosphate Isomerase/Epimerase (YP_324688.1) from Anabaena variabilis.
     3ju2 24.8 2.8 249 275 18 Protein SMC04130 from Sinorhizobium meliloti

     

    Shown below is are ribbon representations of the superimposed structures of target id 396647 (yellow) and PDB id 2zvr, the d-tagatose-3-epimerase from Pseudomonas cichori (cyan).

     

    comparison.png

     

      

     

    The crystallization solution contained 0.2 M MgCl2; therefore, electron density within coordination distance of the sidechains of His 249, Glu 287, Asp 223, and Glu 190 was assigned to a bound magnesium ion on each monomer. Shown below is a representation of the structure in the vicinity of the bound magnesium ion. The position of the bound magnesium in the crystal structure of target id 396647 corresponds to that of an active site manganese atom in the crystal structure of PDB ID 2zvr (cyan struture above). Even though taret ID 396647 is annotated as a hypothetical protein, its crystal structure suggests that it is also a sugar isomerase. Shown below is a representation of the structure of target ID 396647 in the vicinity of the putative active site surrounding the bound magnesium. The red spheres correspond to water molecules.

    Mg.bmp

    Ligand Summary

    Reviews

    References

     

    No references found.

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