.
The Open Protein Structure Annotation Network
PDB Keyword
.

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
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS20885,YP_001182657.1, 3.10.450.50, 325154
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 4
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.67 Rfactor 0.151
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 53.99

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    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
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    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.

    Tag page
    • No tags

    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
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch