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3sb4

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

    Title Crystal structure of a Hypothetical leucine rich repeat protein (BT_1240) from Bacteroides thetaiotaomicron VPI-5482 at 1.99 A resolution. To be published
    Site JCSG
    PDB Id 3sb4 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS62796,NP_810153.1
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.75 Rfactor 0.1680
    Waters
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    Solvent Content 55.31

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3sb4

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    Protein Summary

     The hypothetical protein BT1240 from Bacteroides thetaiotaomicron is a dimer with a unique 'broken' into 2 parts leucine rich repeat (LLR) beta-helix with irregular crossection. The LRR assignment is confirmed both by sequence and structural similarity to other LRR proteins. This is, as far as I can tell, a first case of such two-subdomain LRR protein, with all the other examples forming a regular, crescent-like structure, seen for instance in the TLR receptor domains. Another unique feature of BT1240-lie LRRs, BT1240 appears to be a divergent member of BspA family of surface receptors present in Trichomonas vaginalis and many other pathogens[Ref]

     

    In addition to the characteristic LEU and ILE repeats (shown in Fig.3), which fill out the helix from 'inside', there is a complementary internal PHE repeat, shown in Fig.1.

     

    Every second, third or fourth residue, predominantly of charged character within each LRR segment of the solenoid, is pointing towards 'outside', contributing to the strongly charged external solenoid surface. The residues inbetween, exclusively of hydrophobic character (LEU,ILE,PHE,VAL,GLY) point towards inside, buiding a strongly conserved part of the soleniod core among the LRR proteins.

     

     

    The kink in the solenoid fold and brake into 2 LRR domains is most probably facilitated by electrostatics with preservation of the parallel character of the beta strands. None of the LEU-repeat structures contains that characteristic fold as this one, among most similar LRR homologs, i.e. 2id5[Ref], 3o53[Ref], 2o6q. The PHE, LEU and ILE 'internal' helix architecture is the most conserved feature among all other homologs received in Dali search, in particular the almost identical helix core of BT1240 and 2o6q (lymphocyte receptor).

     

     

    J.Biol.Chem.282,No9., p.6726-6732[Ref], suggests for the antigen binding site a TYR rich area(3) in the concave part of the toroidal 2o6q helix fold. In our BT1240 the N-terminal distorted part of the beta-helix, building two opposite facing beta-hairpins, contains 5 clustered TYR's:84, 91,97,99,107, which given the open cleft between these hairpins(bottom part of the red molecule in Fig 1.), could accommodate a substrate, being 'driven' by those TYR's. Additional proof for that hypothesis, gives the fo-fc map with yet unknown extended density connecting BTYR107 and BTYR91 and AHIS189, thus tiding the substrate binding with functional dimeric structure of BT1240 (Fig.4). The homology between this bacterial protein from human gut and human protein Lingo-1(2id5), or Hagfish Lymphocyte receptor (2o6q), indicates a functional similarity of the building block represented by the LRR beta-helix in general.

     

    6 bound glycerol molecules in the most 'distorted' clefts on the helix surface are shown below on the scheme of a single monomer (Fig.2)

     

    The last characteristic feature of the BT1240 is the 'mirrored' closure at the C-termini of both molecules, building a parallel strand with LYS residues aligned in an antiparallel fasion between the two protomers in the asymmetric unit.

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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    Files (4)

    FileSizeDateAttached by 
     chimera-1.jpg
    chimera representation of the BT1240 dimer indicating the PHE repeat
    129.61 kB20:37, 3 Mar 2011cbtrameActions
     chimera2.jpg
    chimera scheme of the dimer pointing the LEU and ILE repeats
    213.19 kB20:40, 3 Mar 2011cbtrameActions
     MUS2442.jpg
    MaarkUS representation of one protomer with GOL ligands
    385.88 kB20:38, 3 Mar 2011cbtrameActions
     TYR-cluster.jpg
    N-terminal TYR cluster with unknown density
    562.99 kB20:41, 3 Mar 2011cbtrameActions
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