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The Open Protein Structure Annotation Network
PDB Keyword
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3fmc

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

    Title Crystal structure of putative succinylglutamate desuccinylase / aspartoacylase (YP_926482.1) from Shewanella amazonensis SB2B at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3fmc Target Id 375151
    Molecular Characteristics
    Source Shewanella amazonensis sb2b
    Alias Ids TPS20113,YP_926482.1, 104098 Molecular Weight 40877.72 Da.
    Residues 367 Isoelectric Point 5.92
    Sequence mrvdkhevrvgelaagqplslpvyrfkgkgagpsvyiqanvhgaevqgnaviyqlmkllehyellgdis lvplanplginqksgeftlgrfdpitgvnwnreyldhgfnievwyqehshldddtlitafratlveeca rrlnnpwgvttghrlavtlqsmahradivldlhtgpksckhlycpeyersaaqyfsipytllipnsfgg amdeaafvpwwtlaevasshgrelgvrvsaltlelgsqeridlddaledaegilaylshrgviaetvlp kpmkrygcflknyrkfhapkagmveylgkvgvpmkatdplvnllrldlygtgeeltvlrlpedgvpilh fasasvhqgtelykvmtkvfel
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.80 Rfree 0.187
    Matthews' coefficent 3.42 Rfactor 0.155
    Waters 1796 Solvent Content 63.99

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fmc

    Protein Summary

     Gene Sama_0604 from Shewanella amazonensis SB2B encodes the YP_926482 protein that belongs to the AstE_AspA (Succinylglutamate desuccinylase / Aspartoacylase family) group PF04952 . This family includes Succinylglutamate desuccinylase EC:3.1.-.- that catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway.

    The 3fmc structure assembles as a tetramer in the crystallographic asymmetric unit, which is also a biological unit.

     tetramer_93611_90deg.png

     

    Fig 1. Tetramer structure of 3fmc.

     

    Using 3fmc as query, the best hit from FFAS and Dali is 3cdx (Succinylglutamate desuccinylase/ Aspartoacylase; 2.7A rmsd, 292 Ca aligned, 23% id). The superposition of 3fmc and 3cdx shows that 3fmc contains extra helices as shown below.  

     

     super_3cdx.png

     Fig 2. Superposition of 3fmc (green) with 3cdx (pale cyan).

     The putative active site based on comparisons to similar structures is shown below. Ramachandran outlier residues 174 in all chains, which are supported by electron density, are located in the vicinity of the active site and needed to maintain site geometry.

     

     acrive_97368.png

    Fig 3. Location of putative active site of 3fmc. The conserved residues (Asn100, Asp169, His171 and Glu241) are shown as stick (magenta). SO4 group is shown as red sphere.

    Ligand Summary

    Reviews

    References

     

    No references found.

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