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The Open Protein Structure Annotation Network
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3hn5

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

    Title Crystal structure of BF0290 (YP_210027.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3hn5 Target Id 393155
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS25760,YP_210027.1, 324057 Molecular Weight 24170.75 Da.
    Residues 214 Isoelectric Point 4.89
    Sequence mkdnydapesmltgrvmyngealqlrgneavqlqlyqhgyakhdpinvyvnqdgmysanlfdgeyqmit ksgngpwtsegrdtinvtvagntvqdvevtpyylvrdaqmtlegnkvnasfkvekvagggidrvffmls ttqfvndaehnvdrydetdnldaydetgklytfatrdytdnsmfqtalkrgtlfgriciwpkgsdqgiy skvirlk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.203
    Matthews' coefficent 1.95 Rfactor 0.165
    Waters 417 Solvent Content 36.84

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hn5

    Protein Summary

    Bacteroides fragilis proteins BF0290 is a first solved representative of a new protein family of ~50 proteins, present solely in Bacteroidetes found in human gut microbiome and soil, as well as metagenomics samples from these two environments.  BF0290 was predicted to contain a N-term signal peptide, but this is likely an transmembrane helix anchoring this protein to the outer membrane . The genome context suggests that this protein is  functionally related to a SusC/SusD-like polysaccharide utilisation system and given its position right next to SusD homolog, analogous to SusE, it is probably involved in carbohydrate binding (sus operon consists of (among others) proteins SusC-SusD-SusE, in genomic neighborhood of BF0290 is SusC-homolog - SusD-homolog, BF0290)

    Weak BLAST match to a domain in TonB-dependent receptor (such as for instance TonB-dependent siderophore receptor from Nitrobacter winogradskyi Uniprot: Q3SQY4) is most likely a false positive, as the relevant fragment of TonB-dependent receptor structure has no resemblance to the structure of BF0290. The sequence motif 23-DNx[DE]xPx5G is mostly disordered. It is likely this sequence is used to interact with another protein.

     

    The structures of domain 1 and 2 are structurally similar to many carbohydrate binding proteins (see below), suggesting that this protein may bind carbohydrates.

     

    Considering all the facts, one may speculate that BF0290 and its homologs for a part of a transmembrane protein complex transporting carbohydrates, with BF0290 functioning as a binding module (hypothesis).

     

    Top Dali hits of domain 1:

       1:  1h8l-A  8.6  2.2   74   380   19 CARBOXYPEPTIDASE GP180 RESIDUES 503-882;                   
       2:  1qmu-A  8.6  2.1   74   380   19 CARBOXYPEPTIDASE GP180 RESIDUES 503-882;                   
       3:  2nsm-A  8.5  2.1   72   390   21  CARBOXYPEPTIDASE N CATALYTIC CHAIN;                        
       4:  2pz4-A  8.3  2.2   82   239   18 PROTEIN GBS052;                                            
       5:  3e8v-A  7.9  2.5   75    82    9 POSSIBLE TRANSGLUTAMINASE-FAMILY PROTEIN;                  
       6:  1ti4-F  7.8  2.4   74   274   15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT;               
       7:  1ti6-F  7.8  2.4   74   274   15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT;               
       8:  1r6v-A  7.4  3.0   77   671   13 SUBTILISIN-LIKE SERINE PROTEASE;                           
       9:  1ti2-F  7.4  2.4   74   274   15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT;               
      10:  1nkg-A  7.3  2.3   67   508   19 RHAMNOGALACTURONASE B;                                     
     

    Top Dali hits of domain 2:

       1:  2je8-B  9.0  2.4   92   841   11 BETA-MANNOSIDASE;                                          
       2:  3bga-A  8.9  2.8   98  1003    8 BETA-GALACTOSIDASE;                                        
       3:  2vzv-A  8.3  2.7   91   857   10  EXO-BETA-D-GLUCOSAMINIDASE;                                
       4:  3b4n-A  8.3  2.0   79   314    5 ENDO-PECTATE LYASE;                                        
       5:  3e0g-A  8.0  2.4   88   479    7 LEUKEMIA INHIBITORY FACTOR RECEPTOR;                       
       6:  3b8y-B  8.0  2.3   78   294    6  ENDO-PECTATE LYASE;                                        
       7:  2ibg-A  7.9  2.7   92   214   15  CG9211-PA;                                                 
       8:  1x5k-A  7.4  2.5   87   124   11   NEOGENIN;                                                  
       9:  2dlh-A  7.4  2.4   87   121   11 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA;          
      10:  3f7q-A  7.4  2.7   84   214   10   INTEGRIN BETA-4;                                          

     

    Figure 1. 393155 monomer

    gs13427a.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    gs13427a monomer
    80.92 kB21:37, 28 Apr 2009qxuActions
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