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3lwc

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

    Title Crystal structure of Structural Genomics, unknown function (YP_766765.1) from Rhizobium leguminosarum BV. viciae 3841 at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3lwc Target Id 403814
    Molecular Characteristics
    Source Rhizobium leguminosarum bv. viciae 3841
    Alias Ids TPS29790,YP_766765.1, 2.60.120.10, PF06249 Molecular Weight 12746.70 Da.
    Residues 118 Isoelectric Point 5.27
    Sequence ktmkmrkftiadaslerspgqeadisvgnlvderhggpitigygryapgqsltetmavddvmivlegrl svstdgetvtagpgeivympkgetvtirsheegaltayvtyphwrpaha
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.40 Rfree 0.189
    Matthews' coefficent 2.05 Rfactor 0.181
    Waters 59 Solvent Content 40.02

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lwc

    Protein Summary

    The following content, including sequence alignemnt and figures, is uploaded from Kevin Kai Jin's refinement summary, more discussion about these Eut protein structures will be continuously added very soon

    This target is part of the Pfam EutQ family. It looks like you already solved the first structure in this family (2pyt) but haven't published a paper on it yet. We already have it classified into the Cupin clan. I'm not sure we have much more to say about this one

    Gene YP_766765.1 from bacterial Rhizobium leguminosarum bv. viciae 3841 encodes a protein containing 131 residues with the isoelectric Point of 6.06. NCBI sequence alignment indicates this protein may be ethanolamine utilization protein  from Listeria monocytogenes FSL J1-208 (ZP_05294531.1) with the E-value of 3e-06, belonging to EutQ-superfamily (PF06249).  Protein YP_766765.1 has been assigned to both Cupin_2 (PF) and Cup_3 domain with the fold of TIM-Barrel. Both SSM search and FFAS search can only provide some remote structural homologus with various functionalities. Dali search shows that this protein is a structural homolog to another JCSG target (PDB ID: 2PYT), which is also an ethanolamine utilization protein  from Salmonella typhimurium lt2.  Both of these EuTQ protein structures share similar fold with the polyketide cyclase RemF(PDB ID: 3HT1) from Streptomyces resistomycificus containing an unusual octahedral zinc binding site.   The interface interaction suggests that the biomolecule of protein YP_766765.1 be a dimer.

     

    403814_2.png

    Figure 1. Protein YP_766765.1 carries cupin domain belonging

    to EuTQ protein.

     

    403814_1.png

    Figure 2. The biomolecue of protein YP_766765.1 is a dimer.

     

    403814_3.png

    Figure 3. Protein YP_766765.1 (PDB 3LW, green) is structure homolog to

    2PYT(cyan) and 3HT1(red).

     

    403814_4.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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