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The Open Protein Structure Annotation Network
PDB Keyword
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3jys

    Title Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3jys Target Id 396550
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS26684,YP_001298690.1, BIG_773, 326110 Molecular Weight 56279.75 Da.
    Residues 498 Isoelectric Point 4.72
    Sequence dkaytdaesytkglhkiysvwalsgqdgssssdisgldagntallrcwwtlqeqptdemknawndawct evnymtwttnkvepiegvyqrcmyivalvneflknipnapesidkesyiaqarfnrafayyvlmdmfal ppfiteknysiepaplsredlfnwieaelneikpnlpsprseygvadqavasallarmylnaeiytgka rytecinacnevikagyqladnyadlfkadngenpdtkkeiiypiifdgdktqswgmaaiiigargaed kdvllahsgvdqgwagfratsnlvhlfdfqndeepkaseiqdkrgifydkgrsiditssvsgtfetegw svfkfsnlnsngqpgkntlwvdtdfpmfrlgdiylmyaeavarggegskasaveyinalrkraygddkh nisenwleennfrnlldergrelywegirrtdlvrfdlltsgsytwdfkggintgvgvnkrynvypipv tdltvngnlqqnegy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.198
    Matthews' coefficent 2.40 Rfactor 0.178
    Waters 266 Solvent Content 48.65

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3jys
    1. Glycan recognition by the Bacteroidetes Sus-like systems
    DN Bolam, NM Koropatkin - Current Opinion in Structural Biology, 2012 - Elsevier
     

    Protein Summary

    The protein YP_001298690.1 is annotated as Putative outer membrane protein, probably involved in nutrientbinding. YP_001298690.1 belongs to PFAM PF07980 SusD_RagB.

    The protein is essentially a all-helical protein and most likely exists as a monomer.

    PX9961L.png

    There are several structural homologs of this protein - mostly SUSD proteins, as shown in the table below.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE (JCSG structures highlighted in red)
    1 3ck8 47.6 2.0 454 501 36 SUSD
    2 3ckc 47.4 2.0 450 501 36 SUSD
    3 3ck7 47.4 2.0 450 497 36 SUSD
    4 3ckb 47.2 2.0 450 501 36 SUSD
    5 3ck9 46.9 2.0 454 508 36 SUSD
    6 3hdx 32.3 2.7 392 456 20 SUSD SUPERFAMILY PROTEIN
    7 3fdh 22.9 3.0 362 472 11 SUSD HOMOLOG
    8 3cgh 21.7 3.3 373 507 13 SUSD HOMOLOG
    9 3gzs 21.4 3.3 371 495 15 UNCHARACTERIZED SUSD SUPERFAMILY PROTEIN
    10 3ehn 20.7 3.3 372 514 15 SUSD HOMOLOG

     

    A superposition of these proteins is shown below.

    all.png

    Color scheme: YP_001298690.1 (green), 3cgh (cyan), 3ck7 (lightmagenta), 3ck8 (yellow), 3ck9 (salmon), 3ckb (lightgrey), 3ckc (slate), 3ehn (orange), 3fdh (lime), 3gzs (deepteal), 3hdx (hotpink).

     

    Literature references
    1. Schurmann A, Brauers A, Massmann S, Becker W, Joost HG; , J Biol Chem 1995;270:28982-28988.: Cloning of a novel family of mammalian GTP-binding proteins (RagA, RagBs, RagB1) with remote similarity to the Ras-related GTPases. PUBMED:7499430

    2. Cho KH, Salyers AA; , J Bacteriol 2001;183:7224-7230.: Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron. PUBMED:11717282

    Ligand Summary

    Reviews

    References

     

    No references found.

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    322.8 kB15:24, 4 Aug 2009abhinavkActions
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    136.25 kB15:24, 4 Aug 2009abhinavkActions
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