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The Open Protein Structure Annotation Network
PDB Keyword
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3ele

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

    Title Crystal structure of Amino Transferase (RER070207001803) from Eubacterium rectale at 2.10 A resolution. TO BE PUBLISHED
    Site JCSG
    PDB Id 3ele Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS18344,YP_002936484.1, 3.40.640.10, 85530
    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 2.33 Rfactor 0.173
    Waters
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    Solvent Content 47.11

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3ele
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     

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    Protein Summary

    This protein is most likely an amino transferase on the basis of BLAST, PFAM annotation, and structural homologs.

     A BLAST search identifies this sequence as a member of the Aminotran_1_2 Superfamily (cl00321) from CDD and finds NP_349436.1, an aspartate aminotransferase from Clostridium acetobutylicum ATCC 824, as the closest match.

    This protein also shares sequence similarity with PFAM PF00155. This is a family of Aminotransferase class I and II. Aminotransferases 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. This entry includes proteins from both subfamilies.

    SSM search returns several hits as structural homologs of this protein. A few of these are shown below superimposed on this target (green), aspartate aminotransferase (TM1255) from Thermotoga maritima (yellow, PDB code: 1o4s, TOPSAN page) and alanine aminotransferase from Pyrococcus furiosus Pfu-1397077-001 (pink, PDB code: 1xi9, TOPSAN page). The ligand PLP is shown in stick representation in the active site of the proteins.

    MG3309B_1o4s_1xi9_PLP.png

      

    The protein consists of two domains, shown below, and forms a stable dimer.

    MG3309B.png MG3309B_dimer.png

      

    The ligand PLP (yellow sticks) interacts with both monomers in the dimer (shown below). The interacting residues are rendered in grey sticks and are provided by both chains in the dimer. Residue Tyr 72, at the bottom part of the figure, comes from the other chain and interacts with the phosphate group of PLP.

    MG3309B_PLP.png

      

    The unbiased density modified (DM) map obtained after MAD phasing (and prior to any model building) supports the  modeling of PLP in the active site shown below.

    PLP_DMmap.png

      

      

    References:

    • 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
    • Schwarzenbacher, R.,  Jaroszewski, L.,  von Delft, F.,  Abdubek, P.,  Ambing, E.,  Biorac, T.,  Brinen, L.S.,  Canaves, J.M.,  Cambell, J.,  Chiu, H.J.,  Dai, X.,  Deacon, A.M.,  DiDonato, M.,  Elsliger, M.A.,  Eshagi, S.,  Floyd, R.,  Godzik, A.,  Grittini, C.,  Grzechnik, S.K.,  Hampton, E.,  Karlak, C.,  Klock, H.E.,  Koesema, E.,  Kovarik, J.S.,  Kreusch, A.,  Kuhn, P.,  Lesley, S.A.,  Levin, I., McMullan, D.,  McPhillips, T.M.,  Miller, M.D.,  Morse, A.,  Moy, K.,  Ouyang, J.,  Page, R.,  Quijano, K.,  Robb, A.,  Spraggon, G., Stevens, R.C.,  van den Bedem, H.,  Velasquez, J.,  Vincent, J.,  Wang, X.,  West, B.,  Wolf, G.,  Xu, Q.,  Hodgson, K.O.,  Wooley, J.,  Wilson, I.A.   (2004) Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution  Proteins   55: 759-763



      

    Ligand Summary

    PYRIDOXAL-5*-PHOSPHATE (PLP) in each chain

    Reviews

    References

     

    No references found.

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