The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of SnoaL-like polyketide cyclase (17741376) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3ehc Target Id 390431
    Molecular Characteristics
    Source Agrobacterium tumefaciens str. c58
    Alias Ids TPS14567,17741376, 3.10.450.50, 88975 Molecular Weight 14751.97 Da.
    Residues 127 Isoelectric Point 4.82
    Sequence mqtlndiylayldslnhqafdelgtfvddnvehngrpfglsgyrdmlvkdfadipdlrfeaeilvsdat rlaarlffdctpksifmdlpvngrrvqfcehvfydfeqakirrvwsvldkvaierqlg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.12 Rfree 0.243
    Matthews' coefficent 3.42 Rfactor 0.205
    Waters 485 Solvent Content 64.08

    Ligand Information


    Google Scholar output for 3ehc

    Protein Summary

    Gene Atu3018 from Agrobacterium tumefaciens str. c58 (dupont) translates into the NP_357580 protein that shares sequence similarity with the SnoaL-like polyketide cyclase (PF07366, E-value: 1.2e-49) in Pfam, COG 5485: predicted ester cyclase, and the NTF2_like superfamily (cl09109) from CDD which contains both PF07366 and COG5485.

    3ehc belongs to the SCOP alpha+beta class, NTF2-like superfamily. The protein assembles as two biological dimers in the crystallographic asymmetric unit as shown below.



    Fig. 1 Crystallographic asymmetric unit of 3ehc. Four chains are colored as green, cyan, pink and yellow.


    According to DALI, 3ehc is structurally similar to Aklanonic Acid methyl Ester Cyclase, AknH (PDB:2f98; Z=15.6, rmsd=2.1 for 125 aligned Ca, 14% seq id) ; (PDB:2f99; Z=15.4, rmsd=2.1 for 124 aligned Ca, 15% seq id) and Nogalonic Acid Methyl Ester Cyclase, Snoal (PDB:1sjw, Z=15.4, rmsd=2.1 for 125 aligned Ca, 15% seq id). Superposition of 3ehc with 2f98 is shown below. Please notice that 3ehc doesn't contain the ligand in the active site.





    Fig. 2 Superposition of 3ehc (green) with 2f98 (grey). Substrate (NAME; nogalonic acid methyl ester) of 2f98 is shown as grey stick. In 3ehc there is a small unmodeled electron density found near the ligand binding site. This was not modeled since it didn't have any interaction with the neighboring residues or solvents.

    Ligand Summary




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