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The Open Protein Structure Annotation Network
PDB Keyword
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3ly1

    Title Crystal structure of Putative histidinol-phosphate aminotransferase (YP_050345.1) from Erwinia carotovora atroseptica SCRI1043 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3ly1 Target Id 396273
    Molecular Characteristics
    Source Erwinia carotovora subsp. atroseptica scri1043
    Alias Ids TPS29546,YP_050345.1, 3.40.640.10, 327049 Molecular Weight 38526.13 Da.
    Residues 353 Isoelectric Point 6.21
    Sequence etqpesaaftapstdnpirinfnenplgmspkaqaaardavvkanryakneilmlgnklaahhqveaps illtagssegiraaieayasleaqlvipeltygdgehfakiagmkvtkvkmldnwafdieglkaavaay sgpsivylvnpnnptgtitpadviepwiaskpantmfivdeayaefvndprfrsispmitqgaeniill ktfskihamagmrvgyavahptvialmgryvagekinfsgvdaalasmndsafityskksndvsrqill kaledlklpylpsegnfvfhqlvvplkdyqthmadagvligrafppadnwcrislgtpqemqwvadtmr efrkkswi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.80 Rfree 0.206
    Matthews' coefficent 2.80 Rfactor 0.176
    Waters 1809 Solvent Content 56.15

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The protein YP_050345.1 is annotated as Putative aminotransferase. YP_050345.1 belongs to PFAM PF00155 Aminotran_1_2.

     

    A structural similarity search suggests that this could be a Histidinol-Phosphate Aminotransferase, as shown by the DALI search below.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 3get 42.1 1.9 333 365 23 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
    2 3ffh 39.5 2.0 328 352 24 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
    3 3hdo 37.9 2.2 323 349 23 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
    4 1lc5 37.6 2.1 327 355 22 L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
    5 1lkc 37.5 2.1 330 355 22 L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
    6 1lc8 37.4 2.1 330 356 22 L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
    7 1lc7 37.4 2.1 329 358 22 L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
    8 3ftb 37.3 2.1 325 334 20 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
    9 1fg7 37.0 2.4 322 354 25 HISTIDINOL PHOSPHATE AMINOTRANSFERASE
    10 1o4s 36.8 2.5 333 384 18 ASPARTATE AMINOTRANSFERASE

     

    Further evidence for this protein to be a Histidinol-Phosphate Aminotransferase is lent by the presence of an electron density resembling a-keto glutaric acid - a substrate of this enzyme.

     

    Histidinol-phosphate transaminase (EC 2.6.1.9)  catalyzes the chemical reaction:

    L-histidinol phosphate + 2-oxoglutarate \rightleftharpoons 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate

    The protein is a dimer and binds  Pyridoxal-5*-Phosphate (PLP) and citrate which resembles 2-Oxyglutaric acid.

     

    PX14503B_dimer.png

     

    A close-up view of the active site is shown below.

    PX14503B_PLP_CIT.png


    A superposition with the closest neighbor (3get) is shown below.

    PX14503B_3get.png

    YP_050345.1 (green), 3get (magenta)


    Ligand Summary

    Reviews

    References

     

    No references found.

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