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The Open Protein Structure Annotation Network
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3dxo

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

    Title Crystal structure of SnoaL-like Protein with Unknown Function (17739112) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.70 A resolution. To be published
    Site JCSG
    PDB Id 3dxo Target Id 390424
    Molecular Characteristics
    Source Agrobacterium tumefaciens str. c58
    Alias Ids TPS18191,17739112, 3.10.450.50, 88952 Molecular Weight 13221.97 Da.
    Residues 120 Isoelectric Point 4.86
    Sequence mtqhltiaqtylaawneednerrrhlvgqawaentryvdplmqgegqqgiaamieaarqkfpgyrfvla gtpdghgnftrfswrlispdgddvaggtdvvslntegridnvvgfldgavs
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.70 Rfree 0.262
    Matthews' coefficent 3.63 Rfactor 0.231
    Waters 44 Solvent Content 66.10

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3dxo
    1. Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments
    F Pavelcik, J Vaclavik - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene Atu0744 from Agrobacterium tumefaciens str. c58 (dupont) encodes the NP_353768 protein that shows weak homology (E-value 0.0082) to Pfam family SnoaL (PF07366), formerly known as DUF1486. SnoaL is a polyketide synthase (Sultana 2004) involved in nogalamycin biosynthesis. Nogalamycin is a DNA-binding anthracycline antibiotic with anti-tumor properties.

    The genome neighborhood/context for 3dxo is uncharacterized, as it is the case for many homologs. A Burkholderia homolog (Bcep18194_B0334) shows an RbsD or FucU transport associated protein and a galactarate dehydratase (EC 4.2.1.42) as predicted functional partners. The RbsD/FucU transport protein family (PF05025) is a high affinity multi-protein system implicated in ribose and fucose transport. Another homolog, mll5035 from Mesorhizobium loti, shows a xylose isomerase (EC 5.3.1.5) in its genomic neighborhood.

     

    Pre-SCOP classifies 3dxo in the alpha+beta class, NTF2-like superfamily, Atu0744-like family. FFAS and DALI show significant similarity (Zscr=14-13) of 3dxo to a number of steroid delta-isomerases (EC 5.3.3.1) (PDB id: 1ocv, 1isk, 1ohp, 1ogz, 1c7h, 1ea2, 1cqs, 1w6y, 1e97, 1w00, 1dmq, 1dmm, 1gs3) with sequence identity between 13-15%. Structural superposition of a 3dxo monomer with a 1oh0 monomer shows an rmsd of 1.9 Å over 102 residues. Superposition with another JCSG structure (2rgq) shows 2.0 Å rmsd over 111 residues. Steroid delta-isomerases are implicated in lipid metabolism and transport.

    3dxo shows sequence and structural conservation of the residues important for catalysis (Tyr11, Trp31, Glu40, Pro41) and partially for dimerization (Tyr119) in ketosteroid isomerases. However, the dimerization interface is different than that of conventional enzymes (rmsd 4.1 Å over 201 residues with 1oh0). Dimerization has been shown to be essential for the integrity of the ketoisomerase binding site (Nam 2003).

     

    3dxo forms a dimer that buries 583 Å^2 of solvent-exposed surface.

     

    [describe differences in dimerization - implications?]

    [could this dimer be the result of crystallization constraints, i.e. an artifact?]

    [3en8 is a monomer, 3dxo dimer, 2rgq forms trimers]

    [could differences in dimerization be inducing differences in the identity of the binding site?]

    [is there any precedent for this?]

    [2rgq forms trimers - could it be the other way round, i.e. ligand dictating state and manner of oligomerization?]

    [check conservation of dimerization site residues in well-established keto-steroid isomerases]

    [another possibility would involve certain residues, e.g. aromatics, conserved for the core and possibly too common chemical/structural elements in the ligand, the differences conserved in subfamilies acting to confer specificity]

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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