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The Open Protein Structure Annotation Network
PDB Keyword
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3hdx

    Title Crystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution. To be Published
    Site JCSG
    PDB Id 3hdx Target Id 396191
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25869,NP_809182.1, BIG_773, 332836 Molecular Weight 54730.60 Da.
    Residues 477 Isoelectric Point 5.53
    Sequence asetqqwktledtrsalmgvygltraaladnnthwicgdlrkgdftvykrsdlqavsdnelnkpydllk kvsnwrrfyavinaasvfmekaprtveldrsyseqnlkydiaqvralrafayfymvriwgdvplvtysy dngtfpsmprtdaqtvlsyakaelltaiedlpyqygtqtnlyygsygaqwqgklfnklsaysvlahica wqgnyaeaetysafiidhaseinakytsiadltsetglfysnasvkgsrilgfnfahndneatqsghle qltlayplvqksypeiyiskdslfsiftnfddlrfgiidtikyssyyvqnlneetpvfskikiiqdgsa kdndfgvfgssivftrleditllraealcalnrsteavsylnmirtnrglrevsfkkdfgnnresliae ifeerrrelmgegwrwydlvrrqklmkdneaflrlissggiywpvsediitansqieqnefwk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.160
    Matthews' coefficent 2.16 Rfactor 0.134
    Waters 603 Solvent Content 43.10

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hdx
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    2. Glycan recognition by the Bacteroidetes Sus-like systems
    DN Bolam, NM Koropatkin - Current Opinion in Structural Biology, 2012 - Elsevier
     

    Protein Summary

    NP_809182.1 is a SusD homolog protein and belongs to PFAM PF07980 which contains several proteins with unknown functions.

    This protein is an all helical protein with the exception of one pair of short beta strand, shown below.

    PX14351B.png

    The monomer structure is also the most likely solution oligomeric state according to the crytsal packing analysis.

     

    The structural homologs of this protein are mostlu SusD proteins, as mentioned above and shown by the DALI search.

    DALI Structural Homologs

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3ck8 30.3 2.8 383 501 20 SUSD
    2 3ck7 30.3 2.7 378 497 20 SUSD
    3 3ckc 30.2 2.7 378 500 20 SUSD
    4 3ckb 30.1 2.7 378 501 20 SUSD
    5 3ck9 29.9 2.8 384 508 20 SUSD
    6 3fdh 22.1 3.0 338 472 14 SUSD HOMOLOG
    7 3cgh 19.4 3.3 344 507 14 SUSD HOMOLOG
    8 3ejn 19.2 3.2 318 450 12 SUSD HOMOLOG
    9 2ijp 10.9 4.1 171 217 11 14-3-3 PROTEIN
    10 3efz 10.8 3.7 170 216 11 14-3-3 PROTEIN

     

     

    A superposition of these structures, shown below, suggests that the core structure is conserved. However, there are extensive variations in the arrangement of helices and loops.

    PX14351B_all.png

    Color scheme: NP_809182.1 (green), 2ijp (cyan), 3cgh (lightmagenta), 3ck7 (yellow), 3ck8 (salmon), 3ck9 (lightgrey), 3ckb (slate), 3ckc (orange), 3efz (lime), 3ejn (deepteal), 3fdh (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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    Files (2)

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     PX14351B.png
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    160.92 kB17:03, 29 Apr 2009abhinavkActions
     PX14351B_all.png
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    314.68 kB17:03, 29 Apr 2009abhinavkActions
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