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The Open Protein Structure Annotation Network
PDB Keyword
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3cgh

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

    Title Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules. Acta Crystallogr.,Sect.F 66 1274-1280 2010
    Site JCSG
    PDB Id 3cgh Target Id 389990
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1782,NP_812895.1, 91958 Molecular Weight 57034.46 Da.
    Residues 515 Isoelectric Point 4.94
    Sequence nyeninsnpyeapdlsadgyalgsamnnlagcvvspdvntaqftdcllggplggyfadsnagftetisn fnpkddwsrvflksdkiiptlysnltqvklvsqntndpvpyaiaqvikvaamhrvtdafgpipysqiga ngeiatpydsqevtyntffdelnaaiatlnensneqlvptadyiykgdvkkwirfanslklrlairiay anpvkaqqmaeeavnpanggviesnadnatwnyfetsqnpiyvatrynqvqtsdhggvpcltggdthaa adiicymngykdnrrekfftksewagqdyvgmrrgivipelkttghkysgvniaptsplywmnaaevaf lraegqavfnfsmggtaesfynqgirlsfeqwgadgvedylkddvnkptaytdpagtntyqnalsniti kwndsadkeekqeriivqkwianwqlgneawadfrrtgypklipvkenksggvvdsekgarrmpyplde fvsnkanveyaianylhgadnmatdvwwaskk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.166
    Matthews' coefficent 2.36 Rfactor 0.140
    Waters 705 Solvent Content 47.99

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3cgh
    1. Structure of a SusD Homologue, BT1043, Involved in Mucin O-Glycan Utilization in a Prominent Human Gut Symbiont,
    N Koropatkin, EC Martens, JI Gordon, TJ Smith - Biochemistry, 2009 - ACS Publications
     
    2. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
    C Bakolitsa, Q Xu, CL Rife, P Abdubek - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene BT_3984 Bacteroides thetaiotaomicron VPI-5482 encodes the protein NP_812895 that belongs to the SusD/RagA family (PF07980). SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane. STRING genome context analysis suggests a 0.805 scored link with BT_3983, a putative outer membrane protein involved in nutrient binding.

    NP_812895 is the first structure from PFAM family of SusD-like proteins PF07980, which is a large family with over 2000 members involved in nutrient binding. After being produced by Bacteroides thetaiotaomicron, a human gut bacterium, BT_3984 is secreted and becomes a part of an outer membrane bound carbohydrate binding complex.

    The fold of 3gch consists of two subdomains with some resemblance to two other known folds. The first domain shows a significant structural similarity to SCOP  alpha-alpha-superhelix fold and especially to the TPR-like superfamily, SuSD-like family (Fig 2), with some traces of sequence similarity. The second subdomain shows much weaker similarity to proteins from the SCOP  alpha/alpha toroid fold (Fig 3). In each case, 3gch contains additional elements that are not seen in either of those folds. Dali top hits are with SusD homologs like PDB:3gzs (Z-scr=49), PDB:3fdh (Z-scr=30), PDB:3ihv (Z-scr=20).


    The model solved by JCSG, 3cgh, contains a truncation, with the first 22 amino acids not included in the expression construct. Additionally, residues 23-30 are disordered and not included in the model. There is a zinc atom coordinated by residues HIS 284, CYS 289, GLU 321, and HIS 344.

    Figure 1. Overall fold of 3cgh, with zinc shown in grey.



    Figure 2. Alignment of 3cgh (blue) with 1hz4 (orange) (Dali Z-scr=6.8).


    Figure 3. Alignment of 3cgh (blue) with 1hzf (red) (Dali Z-scr=5.3).

    Ligand Summary

    Zinc is modeled based on an x-ray flourescence scan, anomalous difference maps, and coordination geometry.

    References

    Reviews

    References

     

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