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The Open Protein Structure Annotation Network
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3gff

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

    Title Crystal structure of IroE-like serine hydrolase (NP_718593.1) from SHEWANELLA ONEIDENSIS at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3gff Target Id 379975
    Molecular Characteristics
    Source Shewanella oneidensis mr-1
    Alias Ids TPS24233,NP_718593.1, 87049 Molecular Weight 37460.68 Da.
    Residues 330 Isoelectric Point 6.31
    Sequence mtstsitaveyqskrlesrllketreyvialpegyaqsleaypvvylldgedqfdhmasllqflsqgtm pqipkviivgihntnrmrdytpthtlvlpsgnkgnpqyqhtggagrfldfiekelapsiesqlrtngin vlvghsfgglvamealrtdrplfsaylaldtslwfdsphyltlleervvkgdfkqkqlfmaiannplsp gfgvssyhkdlnlafadkltklapkglgfmakyypeethqsvshiglydgirhlfkdfaidiysdsfsk qqvidqygvlserfghkvtpsqqyleqliqysdrqqlterkqmleglrqhfakd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.12 Rfree 0.241
    Matthews' coefficent 2.23 Rfactor 0.184
    Waters 289 Solvent Content 44.73

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gff
    1. Structural comparison of human mammalian ste20-like kinases
    CJ Record, A Chaikuad, P Rellos, S Das, ACW Pike - PloS one, 2010 - dx.plos.org
     

    Protein Summary

    Pfam update: This protein is now in family: Family: Esterase (PF00756).

    This is annotated as a hypothetical protein of unknown function belonging to Pfam PF00756 consisting of putative esterases. Based on structural comparisons and discussions presented below, from the crystal structure, this protein is likely to be an IroE-like serine hydrolase (alpha/beta hydrolase).

    It is present as a dimer in the crystal structure and crystal packing analysis and static light scattering suggest that this dimer should be oligomeric form in solution.

    Imidazole (IMD) molecules from the crystallization condition (light blue spheres) have been modeled into a pocket surrounded by His 143, Ser144, Phe 145, His 215, Trp 172 and His 246 (cyan sticks). The dimeric interface is made of residues His56, Phe 63, His251 and Tyr 255 (green sticks) and a salt bridge between Arg259 and Glu244 (red sticks):

    Fig1.png

    A search for other proteins of similar structure using the EBI-SSM server returns a single significant hit with the IroE protein from Bacillus cereus (PDB id 2qm0, Q-score=0.44, rmsd=1.83A over 221 aligned residues). The top hits with FFAS (links above) are also with the same protein including PDB ids 2qm0 and 2gzr (native) and 2gzs (complex with DFP, diisopropyl phosphonate) (Ref1).

    The IroE protein is used by bacteria to scavenge iron from the environment by binding to siderophores (Ref1). The active site of IroE is similar to that of the Fes protein (PDB id 2b20).

    A comparison of this protein structure with that of the IroE (grey) bound to DFP (PDB id 2gzs) shows that the IMD in this protein structure is bound in the same location as the DFP (blue spheres)  and the surrounding residues are also conserved. However, this protein is larger than the IroE protein.

    Fig2.png

     

     His 143, Ser144, Phe 145 and His246 are conserved in the IroE as His 188, Ser 189 , Tyr 190 and His287:

    Fig3.2.png

     

    Ser 189 and His 287 comprise an atypical catalytic dyad in the IroE.

    Also, in the IroE, Asp90 anchors Arg130 in the catalytic site. These 2 residues are also conserved in our protein as Asp49 and Arg85 (yellow sticks).

    Fig4.png

     

    Based on conservation of overall structure and especially putative active site cavity and residues, it is likely that this protein is an IroE or IroE-like protein which makes it a serine hydrolase. IroE, IroD and Fes are the three serine hydrolases that have been characterized as belonging to this iron scavenging pathway (Ref1). Since this protein also has two other residues (Trp172 and His 215) not seen in the IroE, this protein likely uses a different substrate/ligand.

     

    References:

    1. Larsen, N.A.,  Lin, H.,  Wei, R.,  Fischbach, M.A.,  Walsh, C.T. (2006) Structural Characterization of Enterobactin Hydrolase IroE. Biochemistry 45: 10184-10190

    Ligand Summary

    Imidazole (IMD) at the putative active site.

    Reviews

    References

     

    No references found.

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