.
The Open Protein Structure Annotation Network
PDB Keyword
.

3nrd

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

    Title Crystal structure of a histidine triad (HIT) protein (SMc02904) from SINORHIZOBIUM MELILOTI 1021 at 2.06 A resolution. To be published
    Site JCSG
    PDB Id 3nrd 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)
    TPS30786,NP_384335.1, _0064.001425_, 325127
    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 2.37 Rfactor 0.167
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 48.10

    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 3nrd
    1. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    2. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     

    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

    Protein SMc02904 (JCSG target accession code MJ9307D, GenBank accession code NP_384335.1) is a 134-residue protein from Sinorhizobium meliloti, a Gram-negative nitrogen-fixing bacterium that is a symbiant with certain legumes.

    Protein SMc02904 is annotated as a hypothetical protein belonging to Pfam PF01230, which is a family of proteins containing the histidine triad (HIT) motif His-x-His-x-His-x-x (where x is a hydrophobic amino acid).  Members of this superfamily are highly conserved as nucleotide-binding proteins in a variety of organisms [Ref].

    Although SMc02904, does not contain this exact HIT sequence motif, a region of SMc02904 (residues 92-98) contains a similar motif, with the sequence His-Val-His-Val-Ile-Ala-Arg.  This region contains two of the three histidines of the canonical HIT motif.  The third His in the HIT motif is replaced with an Ile instead in the case of SMc02904.

    The structure of SMc02904 was solved by the Se-MAD method to a resolution of 2.06 Angstroms and reveals an alpha/beta fold that belongs to the HIT-like superfamily in the SCOP classification scheme (Figure 1).

    Figure 1.  Structure of protein SMc02904  monomer: (a) gradiently colored from the N- (blue) to the C-terminus (red).

     

    MJ9307D-gradient.png

     

    Crystal packing as well as analytic size exclusion chromatography (anSEC) analyses suggest that the significant oligomeric form of SMc02904 in solution is a dimer, consistent with other members of this protein family (Figure 2).

    Figure 2.  Quaternary structure of SMc02904 is a dimer.  Monomers A and B are colored orange and blue, respectively.

    MJ9307D-dimer.png

     

    A DALI search reveals all of the closest structural neighbors to be of the HIT protein family, with histidine triad proteins blr8122 from Bradyrhizobium japonicum (PDB id 3i4s, sequence id 42% over 132 C-alpha atoms) and VfR176 from Vibrio fischeri (PDB id 3i24, sequence id 39% over 132 C-alpha atoms) being the most similar in terms of both structure and sequence (Table 1 and Figure 3).

    Table 1.  Best structural matches to SMc02904 as assessed by DALI.  Structural neighbors color-highlighted in the table are superimposed with SMc02904 in Figure 3.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3i4s 24.5 0.8 132 134 42 HISTIDINE TRIAD PROTEIN
    2 3i24 21.5 1.3 132 143 39 HIT FAMILY HYDROLASE
    3 2oik 14.8 2.4 119 139 21 HISTIDINE TRIAD (HIT) PROTEIN (Topsan)
    4 3lb5 13.6 2.7 119 136 17 HIT-LIKE PROTEIN INVOLVED IN CELL-CYCLE
    5 4fit 13.2 2.5 114 126 21 FRAGILE HISTIDINE TRIAD PROTEIN [Ref]
    6 2fit 13.2 2.5 117 130 21 FRAGILE HISTIDINE PROTEIN [Ref]
    7 1fit 13.2 2.4 114 126 22 FRAGILE HISTIDINE PROTEIN [Ref]
    8 5fit 13.1 2.4 114 126 22 FRAGILE HISTIDINE TRIAD PROTEIN [Ref]
    9 2eo4 13.0 2.7 116 149 20 150AA LONG HYPOTHETICAL HISTIDINE TRIAD
    10 6fit 12.9 2.5 113 125 21 FRAGILE HISTIDINE TRIAD PROTEIN [Ref]

     

    Figure 3.  Superposition of SMc02904 monomer (yellow) with top structural neighbors 3i4s (blue), 3i24 (red), and 2oik (green).

    MJ9307D-superpose.png

    .

    Ligand Summary

    Reviews

    References

     

    1. (No Results)

       


      Discuss this publication
    2. (No Results)

       


      Discuss this publication
    3. (No Results)

       


      Discuss this publication
    Tag page
    • No tags
    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