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The Open Protein Structure Annotation Network
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3ty1

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

    Title Crystal structure of a Hypothetical aldose 1-epimerase (KPN_04629) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3ty1 Target Id 390294
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS7705,YP_001338247.1, 285606 Molecular Weight 42490.69 Da.
    Residues 383 Isoelectric Point 5.92
    Sequence aktwvltnaeegidkgnwqinsdqlkvkdhafsieqkvlhggkqegskiltihskdgltitlsptrgmn llriegfgsrmgwdspvkevvnpafinlesrnglgwlegfnemmvrcgyewtghpvtadgqiytlhgka gntpaslvevevadsapyeirirglvkestfkkadlqtltelryvpgsnsfslhdvltnhadyphdyqi iyhsnfgtpileegarflapissispfndyaksglktwqtyqgptkdfdemvfniqpladenhqtlaav vnkagdkgasiqfdtrqlpvltlwkntdtvkqgyvtgiepgtsyaypvtierkqkrvkqlqpgasaqfd ltytllhdsaqvaaveqkiakiqgdnkvaenetpiake
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 1.90 Rfree 0.1931
    Matthews' coefficent 2.86 Rfactor 0.1581
    Waters 795 Solvent Content 56.93

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ty1

    Protein Summary

    Pfam update: I have built a family from it that overlaps with Aldose_epimerase. thus it has gone into the Galactose Mutarotase-like superfamily clan. I have called it DUF4432, PF14486. Several of the members were subnamed DeoX, but I could find no evidence for more details on this as all family members were predicted. There are other structures in the Aldose-epimerase family, but obviously the exact structure of this one will be of interest for its further characterisation.

    This protein is annotated as a putative thioredoxin-like protein. It is present as a trimer in the crystal structure:

     

    Fig1.pngFig2.png

     

    Top hits to other proteins of similar structure (using EBI SSM/PDBeFOLD server) are to PDB ids 3k25, 2htb (putative mutarotase), 3os7 (galactose mutarotase-like protein), 3nre (putative aldose 1-epimerase), etc. The Q-scores for these hits are 0.30-0.34, r.m.s.d.s from ~2.2-2.5A, and sequence identities in the 12-14% range. Most of them are structural genomics structures and 3os7 and 3nre are structures determined by JCSG. A detailed report for the 3nre is available on its TOPSAN page alongwith Pfam classification. It is not clear whether this protein and 3nre will be in the same Pfam since their sequence identity is very low, however there are strong structural similarities.

    When this protein structure is superimposed on that of galactose mutarotase (PDB 1l7j), the structural similarity is clear:

    Fig3_on_1L7J.png

    The Arg71, His96, His170, Asp243 and Glu304 of the mutarotase implicated in achoring sugar are partially conserved in this protein as His142, His154, His229 and Glu334. The residue corresponding to Asp243 in 1l7j is present here as Val278, but it could be that the nearbby Glu276 in this protein could have similar function as the Asp243:

    Fig4_putativeactivesite.png

    A sulfate molecule (red) from the crystallization condition has been modeled into electron density at this site.

    Ligand Summary

    Reviews

    References

     

    No references found.

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