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The Open Protein Structure Annotation Network
PDB Keyword
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3lza

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

    Title CRYSTAL STRUCTURE OF PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE (YP_563807.1) FROM SHEWANELLA DENITRIFICANS OS-217 AT 1.70 A RESOLUTION. To be published
    Site JCSG
    PDB Id 3lza Target Id 396443
    Molecular Characteristics
    Source Shewanella denitrificans os217
    Alias Ids TPS26665,SDEN_20JUL04_CONTIG92_REVISED_GENE3346, 3.10.450.50, 327676 Molecular Weight 16035.35 Da.
    Residues 140 Isoelectric Point 5.49
    Sequence kvgdrpieqqlalgyikaltehdyqtlskyynrdsvfydktadtkyigtrsiiaflqrshegvlefdfn iehmfntgplvvmignyhlrgpgeqfgkpgkiidiaipgvttlkfdpntqrlteqvdlmdyqtmsdqlq sq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.70 Rfree 0.238
    Matthews' coefficent 2.17 Rfactor 0.193
    Waters 570 Solvent Content 43.22

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lza
    1. Insights from the sea: Structural biology of marine polyketide synthases
    DL Akey, JJ Gehret, D Khare, JL Smith - Natural Product Reports, 2012 - pubs.rsc.org
     

    Protein Summary

    Gene Sden_2805 from Shewanella denitrificans os-217 translates into the YP_563807 protein that belongs to the SnoaL-like polyketide cyclase (PF07366). Its genome neighborhood shows a possible functional link (score 0.87) with the UPF0126 protein Sden_2804.

    3lza structure corresponds to the C-terminal fragment (18-157) of YP_563807. Pre-SCOP classifies 3lza in the alpha+beta class, NTF2-like superfamily, limonene-1,2-epoxide hydrolase family (?).

    The protein assembles as a dimer in the crystal structure, shown below.

    PX14652B_dimer.png

    The monomer looks like a barrel composed of six stands on one side and three helices on the other side forming the barrel.

     

    The closest structural neighbor of this protein (green) is another JCSG protein, 3gzb (magenta), with 70% sequence identity and rmsd of 0.6 A over 137 residues, shown below.

    PX14652B_3gzb.png

     

    Top 10 hits from a DALI search is shown below.

    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 3gzb 25.8 0.6 137 137 70 PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE
    2 3i0y 16.7 2.1 130 136 15 PUTATIVE POLYKETIDE CYCLASE
    3 3f7x 16.4 1.9 127 133 9 PUTATIVE POLYKETIDE CYCLASE
    4 2bng 16.4 1.9 122 132 19 MB2760
    5 3f8h 15.8 2.4 130 136 9 PUTATIVE POLYKETIDE CYCLASE
    6 2z76 15.6 2.0 122 131 13 PUTATIVE STEROID ISOMERASE
    7 3f9s 15.5 2.1 132 143 18 PUTATIVE POLYKETIDE CYCLASE
    8 2z77 15.5 2.3 124 133 13 PUTATIVE STEROID ISOMERASE
    9 2z7a 15.4 1.8 120 133 13 PUTATIVE STEROID ISOMERASE
    10 1nww 15.1 2.1 124 145 15 LIMONENE-1,2-EPOXIDE HYDROLASE

    Ligand Summary

    Reviews

    References

     

    No references found.

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