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The Open Protein Structure Annotation Network
PDB Keyword
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3gzb

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

    Title Crystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from Shewanella putrefaciens CN-32 at 1.44 A resolution. To be published
    Site JCSG
    PDB Id 3gzb Target Id 391458
    Molecular Characteristics
    Source Shewanella putrefaciens cn-32
    Alias Ids TPS20885,YP_001182657.1, 3.10.450.50, 325154 Molecular Weight 17446.06 Da.
    Residues 153 Isoelectric Point 5.45
    Sequence mfaslvipvsaqansgempqeqqlavkymdaltehdyktlitfynrdsiffdktanrkytggrfiidfl erahqgvleydfniehmynagslvvmignyhfkgpgeqfgkpgkiidvaipavtslkldmlnrrvtehv dlidyqtmsdqlamq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.44 Rfree 0.174
    Matthews' coefficent 2.67 Rfactor 0.151
    Waters 1754 Solvent Content 53.99

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gzb
    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 Sputcn32_1130 from Shewanella putrefaciens cn-32 translates into the YP_001182657 protein that has a weak hit (e-val=0.0001) with the SnoaL-like polyketide cyclase family (PF07366). There are only a few close homologs in Shewanella; one protein (score 0.6) in the neighbourhood is annotated as cobalamin biosynthesis protein ChiB (Sputcn32_1133).

    Pre-SCOP classifies 3gzb in the alpha+beta class, NTF2-like superfamily, limonene-1,2-epoxide hydrolase family (?). DALI top hits are with putative polyketide cyclases like 3i0y, 3f7z and 2bng (Z=16). 3gzb is structurally similar to the epoxide hydrolase (2bng, rmsd 2.03 for 118 aligned Ca atoms, i.e. NTF2-like, PUBMED), but with different active site (e.g. Arg91 of 2bng is not present in 3gzb). One residue, Asp139, is conserved (Figure 1). The active site cavity of 3gzb is mainly hydrophobic (Figure 2). The protein is likely to function as a dimer, like 2bng. 3gzb putative active site contains MPD which may mimic the substrate.

     

     

     

    Figure 1. Monomer of 3gzb with residue Asp139 depicted as spheres

     

     mg14652a.png

    Figure 2. 3gzb surface representation shows a well defined cavity for a putative active site location

    mg14652a-surf.png 

     JCSG has solved many structures of NTF2 like proteins, so it may be worthwhile to consider them as a group.

     

    Johansson, P.,  Unge, T.,  Cronin, A.,  Arand, M.,  Bergfors, T.,  Jones, T.A.,  Mowbray, S.L. (2005) Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function. J.Mol.Biol. 351: 1048-1056

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
    mg14652a-surf.png
    active site pocket
    209.8 kB00:03, 3 Mar 2009qxuActions
     mg14652a.png
    monomer of 391458 with asp139 as spheres
    107.34 kB00:02, 3 Mar 2009qxuActions
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