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3nre

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

    Title Crystal structure of a Putative aldose 1-epimerase (b2544) from ESCHERICHIA COLI K12 at 1.59 A resolution. To be published
    Site JCSG
    PDB Id 3nre Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS29650,NP_417039.1, _0078.001791_
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 4
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.74 Rfactor 0.161
    Waters
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    Solvent Content 55.17

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3nre
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    3. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     

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    Protein Summary

    Pfam update: This sequence has been assigned to the Aldose_epim (PF01263) family, with a high level of certainty.

    There are 4 protein molecules in the asymmetric unit in the crystal structure, but crystal packing analysis suggests a monomer as the solution state form. Analytical SEC also supports the assignment of a monomer as the significant oligomeric form in solution.

    The structure is almost all beta-strands organized into 2 main beta-sheets resembling a beta-sandwich.

    Fig1.png

    A search with SSM of other proteins that are most closely related in structure to this target results in significant hits (Q-score 0.44 and 0.50, respectively and r.m.s.d of ~2.0A) to a GalM/Aldose epimerase homolog (PDB id 1lur) and a galactose mutarotase related enzyme (PDB id 3dcd). Both of these structures are from structural genomics centers.

    According to FFAS (link above), the top closely related proteins to this target are PDB ids 1lur, 3k25 (another structural genomics structure) and 2ciq (Ref1). Based on the comparison of this protein to 2ciq, the catalytic residues here are likely to be Hisxx and Gluxx, which are the catalytic acid and base, similar to that found in the galactose mutarotase (PDB 1l7j, Ref2).

    It should be noted that the overall sequence identity of this protein with the 2ciq or 1l7j is only ~15%.

    As in the 1l7j protein structure that showed Pro67 and Lys136 as cis-peptides, this protein also has cis-peptides at Val51->Pro52 and Thr226->Pro227. The galactose mutarotase residues implicated in achoring with the sugar are Arg71, His96, His170, Asp243 and Glu304 (Ref2). His96 and His170 have been found to be conserved in mutarotase proteins.

    The corresponding residues in this protein are Arg56, His83, His148, Asn200 and Glu253 and are almost strictly conserved. The presence of His83 and His170 suggests that this protein is also a mutarotase.

    5mM D-glucose was added as co-crystallization agent during crystallization setup, but this is not seen bound at the active site. However, the active site does show partially ordered electron density that has been modeled as PEG molecules that are present in the crystallization and cryoprotectant conditions.

    Putative active site residues:

    Fig2_activesite.png 

     

    References:

    1. J. Biol Chem. 2006 Oct 6;281(40):30175-85. Epub 2006 Jul 20.Structure-based functional annotation: yeast ymr099c codes for a D-hexose-6-phosphate mutarotase. Graille, M. , et. al.

     

    2. J Biol Chem. 2002 Jun 7;277(23):20854-61. Epub 2002 Mar 20.High resolution X-ray structure of galactose mutarotase from Lactococcus lactis. Thoden, JB and Holden, HM.

    Ligand Summary

    Reviews

    References

     

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    321.16 kB22:15, 28 Apr 2010debanuActions
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