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The Open Protein Structure Annotation Network
PDB Keyword
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3g7q

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

    Title Crystal structure of valine-pyruvate aminotransferase AvtA (NP_462565.1) from Salmonella typhimurium LT2 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3g7q Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS20897,NP_462565.1, 3.40.640.10, 325186
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.94 Rfactor 0.17797
    Waters
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    Solvent Content 58.23

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3g7q

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    Protein Summary

    NP_462565.1 encodes a protein with 416 residues with a conserved domain belong to AAT_I superfamily. Both NCI blast sequence alignment and Dali search results indicate this protein as an aminotranferase. This protein is  a structural homolog to 1B5O and 1X0M suggested by FFAS and Dali, respectively. There is only one subunit of NP_462565.1 in each asymmetric unit. The biomolecule of this target is suggested a dimer by PISA.

    391498_1.png

     

    Figure 1. Protein NP_462565.1 carries a single domain belong to the AAT_I superfamily.

     

    391498_2.png

     

    Figure 2. The biomolecule of NP_462565.1 is a dimer suggested by PISA.

     

     

    391498_3.png

     

     

     

    Figure 3.   Protein NP_462565.1(green) is structure homolog to 1B5O (Yellow) and 1X0M(Magenta).
     

     

    Annotation by Piotr Kozbial:

    This protein is annotated as valine-pyruvate aminotransferase AvtA by KEGG and is similar to aspartate aminotransferases and their active site cleft, as shown below for PDB:1ix7 (source SuMO server):

      AvtA 1IX7 - MAE Deformation (+ coef.) Deviation (Å) Depth difference Weight
    delta_minus backbone GLY 38 A backbone GLY 38 A 7.9% (3.42) 0.435 0.060 0.6
    aromatic #2 TYR 137 A penta#2 TRP 140 A 11% (5.29) 0.468 0.020 0.9
    amide   ASN 190 A   ASN 194 A 6.9% (8.01) 0.205 0.008 0.75
    delta_minus   TYR 221 A   TYR 225 A 9.6% (3.99) 0.734 0.013 0.6
    aromatic #1 PHE 340 A #1 PHE 360 A 8.7% (5.77) 0.300 0.003 0.9
    delta_plus h12 ARG 388 A h22 ARG 386 A 15% (4.10) 1.104 0.002 0.6

     

    Similarly AvtA is similar to aspartate aminotransferase PDB:1asl (source SuMO server).

     

      AvtA 1ASL - AMA Deformation (+ coef.) Deviation (Å) Depth difference Weight
    amide   ASN 190 A   ASN 194 A 8.2% (8.51) 0.609 0.024 0.75
    delta_minus   TYR 221 A   TYR 225 A 11% (4.52) 0.884 0.033 0.6
    hydroxyl   TYR 221 A   TYR 225 A 11% (4.90) 0.884 0.033 0.65
    aromatic #1 PHE 340 A #2 PHE 360 A 8.1% (6.66) 0.094 0.012 0.9
    delta_plus h12 ARG 388 A h12 ARG 386 A 15% (4.05) 1.361 0.022 0.6
    guanidinium   ARG 388 A   ARG 386 A 5.7% (5.20) 0.221 0.011 0.85

     

    In addition to residues from cleft listed above, there is much smaller adjucent cleft with Cys257, Asp104 and Gly282.

    AvtA is a member of COG3977 (source NCBI) and belongs to:
    (a) 'valine, leucine and isoleucine biosynthesis pathway' (source KEGG database and STRING server),
    (b)inter-pathway connection between 'valine, leucine and isoleucine degradation' and 'valine, leucine and isoleucine biosynthesis'  (source KEGG database and STRING server),
    (c) alanine biosynthesis I pathway (source BioCyc/EcoCyc Pathways and STRING server).

    End of Piotr Kozbial's annotation.

     

    References,

    1.     Ura, H.,  Nakai, T.,  Kawaguchi, S.I.,  Miyahara, I.,  Hirotsu, K.,  Kuramitsu, S.   (2001) Substrate recognition mechanism of thermophilic dual-substrate enzyme  J.BIOCHEM.(TOKYO)   130: 89-98   
     
    2.     Chon, H.,  Matsumura, H.,  Koga, Y.,  Takano, K.,  Kanaya, S.   (2005) Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution  Proteins   61: 685-688   
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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