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The Open Protein Structure Annotation Network
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3bww

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

    Title Crystal structure of protein of unknown function (DUF692/COG3220) (YP_719350.1) from Haemophilus somnus 129PT at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3bww Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1635,HSOM_08NOV04_CONTIG98_REVISED_GENE911, PF05114, 91937
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.37 Rfactor 0.195
    Waters
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    Solvent Content 48.18

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3bww
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    Gene HS_1138 (locus YP_719350, Entrez GeneOD  4240639, targetDB ID 374865) from Haemophilus somnus 129pt encodes a protein from PFAM family PF05114 (DUF692/COG3220), a large (>400 members) family of hypothetical proteins, mostly from bacteria but with two eukaryotic homologs - in Plasmodium and castor beans . 3bww is the first solved structure from this family. Distant homology analysis by FFAS sees similarity to endonucleases (score -23.3, sequence id 12% to 1qtw), but also to isomerases and epimerases. Some of the homologs (for instance NEISUBOT_03420 from Neisseria subflava NJ9703) are annotated as AP endonucleases, type 2, but the source of this annotation is not clear.


    The STRING server analysis of similar proteins in related species of
    Haemophilus found several functionally associated proteins (such as: HI1599HI1601, HI1602, and HI1459-probable RNA polymerase sigma factor). The analysis of functional associations may be helpful to indicate the process or metabolic pathway that require proteins that are otherwise functionally uncharacterized. In this case the associations observed in the related species indicates that DUF692 may be involved in the protection or repair of DNA that is essential for optimal acid resistance (see: Cotter and Hill ,2003), or alternatively in repair of oxidative damage (see: Farr and Kogoma, 1991).

    Pre-SCOP classifies 3bww in the alpha/beta class, TIM barrel fold, xylose isomerase-like superfamily, IolI-like family. DALI top hits are with IolI protein

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    (Z=18), tagatose epimerase
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    (Z=17) and TM0416
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    (Z=16).

    The figure depicting invariant and highly conserved residues in 3bww (using data from this alignment) is shown below. Interestingly, Glu-138 is the only residue conserved in all proteins from this and related PFAM families (anything special about the function of this residue in better characterized members of these families?) Please note that the 3bww structure corresponds to fragment 62-367 of the YP_719350 protein and the numbering below refers to the 3bww structure, not to the wildtype protein.



    Figure showing conserved residues (top view).

    Figure showing conserved residues (side view).

    Ligand Summary



    References

    Reviews

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