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The Open Protein Structure Annotation Network
PDB Keyword
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3hyn

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

    3hyn

    Title Crystal structure of Putative signal transduction protein (YP_002936568.1) from Eubacterium rectale at 1.20 A resolution. To be published
    Site JCSG
    PDB Id 3hyn Target Id 391897
    Molecular Characteristics
    Source Eubacterium rectale atcc 33656
    Alias Ids TPS26537,YP_002936568.1, 325552 Molecular Weight 21672.20 Da.
    Residues 188 Isoelectric Point 6.08
    Sequence msyqnanysafyvsepfsesnlgansthdfvyynmlrmwkgednsfpfndahdktynvrdgsdwektlk prlhtrldnskniilflssitansralreemnygigtkglpviviypdydkksdivdsngnfkkqikdl wdklpafrdnmssvatlhipctksviisalnnedfmvntmadaekyyykp
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.20 Rfree 0.139
    Matthews' coefficent 1.84 Rfactor 0.117
    Waters 308 Solvent Content 33.22

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hyn

    Protein Summary

    The EUBREC_0645 gene translates into the YP_002936568 protein from Eubacterium rectale, the most abundant member of Firmicutes phyla in the human gut, and it is the first solved representative of the bacterial TIR-like domain family (DUF1863/PF08937, e-value=0.00017). As expected, it adopts a three layered alpha/beta fold, with a central beta-strands, but it contains additional structural elements as compared to classical TIR domains.  

    TIR domain proteins play an important role in animal immunity signaling pathways and several bacterial TIR proteins were shown to function as virulence factors, suppressing human innate immunity response. It is therefore intriguing to find such protein in a dominant human symbiont.

    Interestingly, 3hyn is structurally most similar to nucleotide binding proteins, not to the TIR domain (DALI top hit, 3ehd, belongs to the nucleoside 2-deoxyribosyl transferase family PF05014). This apparent discrepancy between structural and sequence based similarities is really intriguing and requires further analysis. 

     

    Dali hits for structural similarity search:

    No: Chain Z rmsd lali nres %id PDB Description
    1: 3ehd-A 9.0 3.2 127 158 13 PDB MOLECULE: UNCHARACTERIZED CONSERVED PROTEIN;
    2: 1ha3-B 8.7 3.4 130 379 12 PDB MOLECULE: ELONGATION FACTOR TU;
    3: 1t3g-A 8.5 3.6 124 152 9 PDB MOLECULE: X-LINKED INTERLEUKIN-1 RECEPTOR ACCESSORY
    4: 1dar 8.4 3.0 124 615 7 PDB MOLECULE: ELONGATION FACTOR G;
    5: 2ywf-A 8.4 3.3 124 532 10 PDB MOLECULE: GTP-BINDING PROTEIN LEPA;
    6: 1zun-B 8.3 3.3 131 394 10 PDB MOLECULE: SULFATE ADENYLYLTRANSFERASE SUBUNIT 2;
    7: 1f60-A 8.2 3.3 126 440 12 PDB MOLECULE: ELONGATION FACTOR EEF1A;
    8: 1f8x-A 8.2 3.0 121 156 12 PDB MOLECULE: NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE;
    9: 1s2d-B 8.1 3.3 126 167 10 PDB MOLECULE: PURINE TRANS DEOXYRIBOSYLASE;
    10: 1mky-A 8.0 3.6 131 407 11 PDB MOLECULE: PROBABLE GTP-BINDING PROTEIN ENGA;
    11: 1nni-1 7.9 3.3 129 171 11 PDB MOLECULE: HYPOTHETICAL PROTEIN YHDA;
    12: 3deg-C 7.9 2.9 116 545 8 PDB MOLECULE: A/L-TRNA;
    13: 1b23-P 7.8 3.6 127 405 11 PDB MOLECULE: ELONGATION FACTOR TU;
    14: 2gej-A 7.7 3.8 133 361 9 PDB MOLECULE: PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PIMA);
    15: 2elf-A 7.7 3.6 124 348 10 PDB MOLECULE: PROTEIN TRANSLATION ELONGATION FACTOR 1A;

     

    Figure 1. Monomer of 3hyn

    fr15091a.png

     

    Analysis of sequence conservation among homologs indicated that a cluster of buried hydrophilic residues around H56 are highly conserved. 

    Ligand Summary

     

     

    Reviews

    References

     

    No references found.

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    Files (1)

    FileSizeDateAttached by 
     fr15091a.png
    391897 monomer
    274.73 kB20:55, 18 May 2009qxuActions
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