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The Open Protein Structure Annotation Network
PDB Keyword
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3g0t

    Title Crystal structure of putative aspartate aminotransferase (NP_905498.1) from Porphyromonas gingivalis W83 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3g0t Target Id 391161
    Molecular Characteristics
    Source Porphyromonas gingivalis w83
    Alias Ids TPS18336,NP_905498.1, 3.40.640.10, 291231 Molecular Weight 49287.86 Da.
    Residues 436 Isoelectric Point 5.92
    Sequence mnfpideklirekqnelhikdlgmasirdlvalvtnlekatgtkfcrmemgvpglpapqigieteiqkl regvasiypnldglpelkqeasrfaklfvnidiparacvptvgsmqgcfvsflvanrthknreygtlfi dpgfnlnklqcrilgqkfesfdlfeyrgeklreklesylqtgqfcsiiysnpnnptwqcmtdeelriig elatkhdviviedlayfgmdfrkdyshpgeplyqpsvanytdnyilalssskafsyagqrigvlmisgk lyereypdleesfgrlrfgealsssalyalssgathsaqwgmaamlkacndgeynfrdsvieygrkari mkkmfldngfnivydkdgnepladgfyftvgykgmdsskliekfvrygmcaitlkttgskrneamrict sllpesqfpdlekrlqmlnaeg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.75 Rfree 0.171
    Matthews' coefficent 2.44 Rfactor 0.137
    Waters 1151 Solvent Content 49.58

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3g0t

    Protein Summary

    NP_905498.1 is annotated as an aminotransferase and belongs to PFAM PF00155 of aminotransferases Class I and II. These proteins share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped PUBMED:1990006 into class I and class II.

    The monomer has a typical aminotransferase structure as shown below.

    MG14556B_monomer.png

    The residue LYS 259 is covalently linked with PYRIDOXAL-5'-PHOSPHATE (PLP) via a Schiff base and is shown in stick representation in the figure above. Some additional information on aminotransferases belonging to the clan of PFAM PF00155 can be obtained at another JCSG structure 3fcr.

    The protein assembles as a dimer, shown below, in the crystal structure which is supporded by size exclusion chromatography experiments.

    MG14556B_dimer.png

     

    There are several homologs of this protein. Top ten DAli hits are shown below in the table and a superposition of these structures.

    DALI Structural Homologs

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1b5p 40.6 1.9 356 382 18 ASPARTATE AMINOTRANSFERASE
    2 1bjw 40.5 1.9 356 382 18 ASPARTATE AMINOTRANSFERASE
    3 1gck 40.4 2.2 360 382 18 ASPARTATE AMINOTRANSFERASE
    4 1gc3 40.2 2.1 360 382 18 ASPARTATE AMINOTRANSFERASE
    5 1b5o 40.2 1.9 356 382 18 ASPARTATE AMINOTRANSFERASE
    6 5bj4 40.1 1.9 344 366 18 ASPARTATE AMINOTRANSFERASE
    7 1bkg 40.1 2.1 355 382 18 ASPARTATE AMINOTRANSFERASE
    8 1gc4 40.0 2.2 359 382 18 ASPARTATE AMINOTRANSFERASE
    9 5bj3 39.6 1.8 337 363 18 ASPARTATE AMINOTRANSFERASE
    10 2o0r 39.5 2.2 353 384 18 RV0858C (N-SUCCINYLDIAMINOPIMELATE

     

    all.png

     

    Color scheme in the above figure is: NP_905498.1 (green), 1b5o (cyan), 1b5p (lightmagenta), 1bjw (yellow), 1bkg (salmon), 1gc3 (lightgrey), 1gc4 (slate), 1gck (orange), 2o0r (lime), 5bj3 (deepteal), 5bj4 (hotpink).

     

     

     

    References:

    1. Ko TP, Wu SP, Yang WZ, Tsai H, Yuan HS; , Acta Crystallogr D Biol Crystallogr 1999;55:1474-1477.: Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase. PUBMED:10417420

    2. Nakai T, Okada K, Akutsu S, Miyahara I, Kawaguchi S, Kato R, Kuramitsu S, Hirotsu K; , Biochemistry 1999;38:2413-2424.: Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. PUBMED:10029535

    Ligand Summary

    Reviews

    References

     

    No references found.

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