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3kgw

    Title Crystal structure of Putative aminotransferase (AAH25799.1) from MUS MUSCULUS at 1.65 A resolution. To be published
    Site JCSG
    PDB Id 3kgw Target Id
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    Related PDB Ids 3kgx 
    Molecular Characteristics
    Source
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    Alias Ids
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    TPS30632,19388005, 3.40.640.10, 326071
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.32 Rfactor 0.169
    Waters
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    Solvent Content 47.04

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3kgw
    1. Prediction of mitochondrial matrix protein structures based on feature selection and fragment assembly
    G Asencio-Corts, J Aguilar-Ruiz - , Machine Learning and , 2012 - Springer
     

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    Protein Summary

    Alanine:Glyoxylate Aminotransferase (AGT) is a liver enzyme that converts glyoxylate to glycine. We have determined two structures of AGT from mouse at 1.65 and 1.72 A resolutions respectively under identical conditions except for a slight change in the pH of the crystal growth conditions. The change in pH brings about significant change in the structure around the active site as described later.

     

    The monomer and dimer structures are shown below.

    MA1400A_monomer_chainbow.png MA1400A_dimer_chainbow.png

     

    There are two crytsal structures of this protein. The crystals were grown in slightly different pH (7.8 and 6.2). The change in pH causes significant change in the structures.

    At pH 6.2, a key residue His 105 occupies the active site location where the cofactor PYRIDOXAL-5'-PHOSPHATE (PLP) is supposed to bind. As the pH is raised, the His105 presumbly deprotonates and withdraws out of the active site, thus allowing PLP to bind.

    Although PLP was not added in the crystallization condition, the protein is able to bind endogenous PLP at ph 7.8, albeit to a less extent. The PLP binding process is revealed in this structure since the His105 is observed in two conformations: one in the active site and the other in the location where it should be as observed in other AGT structures from other species.

    The active site is shown here with some of the key residues. The structures are color coded as follows: 402064 (green), 1h0c (lightmagenta), 1j04 (yellow), 1vjo (salmon), 2bkw (lightgrey), 2huf (slate), 2hui (orange), 2huu (lime)

    active_site_labeled.png

     

    In the left panel below 402064 (cyan) is shown with 1h0c (magenta) showing that His 105 occupies the PLP site. On the right panel, the higher pH structure shows that His (green)has withdrawn partially (in two conformers) and PLP has bound.

    active_site.601_602_1h0c_labeled.png

     

    Movement of His105 from the active site causes Tyr 263 to relocate too. Again, in left panel 402064 (cyan) is overlaid on 2huf (yellow) indicating the positions of His and Tyr. At higher pH (right panel), His (green) withdraws, displacing Tyr 263. Again, both His and Tyr are modeled in two conformations revealing the process of relocation.

    tyr_601_602_2huf_labeled.png

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 1j04 61.7 0.8 386 387 76 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    2 1h0c 61.6 0.7 384 385 77 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    3 2huf 58.8 1.0 384 385 47 ALANINE GLYOXYLATE AMINOTRANSFERASE
    4 2huu 58.7 1.0 384 385 47 ALANINE GLYOXYLATE AMINOTRANSFERASE
    5 2hui 58.7 1.0 384 385 47 ALANINE GLYOXYLATE AMINOTRANSFERASE
    6 2ch2 58.4 1.1 383 387 43 3-HYDROXYKYNURENINE TRANSAMINASE
    7 2ch1 58.3 1.1 384 388 43 3-HYDROXYKYNURENINE TRANSAMINASE
    8 1vjo 56.8 1.1 376 377 45 ALANINE--GLYOXYLATE AMINOTRANSFERASE
    9 2yri 48.5 1.4 351 352 34 AMINOTRANSFERASE, CLASS V
    10 2yrr 48.4 1.4 351 352 34 AMINOTRANSFERASE, CLASS V

    Ligand Summary

    Reviews

    References

     

    No references found.

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