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3fzx

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

    Title Crystal structure of putative exported protein with YmcC-like fold (YP_211880.1) from Bacteroides fragilis NCTC 9343 at 2.22 A resolution. To be published
    Site JCSG
    PDB Id 3fzx Target Id 393247
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS24863,YP_211880.1, 324077 Molecular Weight 24606.23 Da.
    Residues 217 Isoelectric Point 4.61
    Sequence aqnqdcafffpnqegeqitrncytadgkltnilvyrvdqayeypsgmevvanytfadaagktlnsgqmv arcsdgnfsmsmgdvatfptalnmmnadvymmgdlmnypdafsnpmnpgdddefddgtlrlyqkgnknn raeisvfdrefvttetvntpagafyctkvkyemniwtpketikgygyewyapnigivrseqynnkkelq sysvlerikk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.22 Rfree 0.250
    Matthews' coefficent 2.93 Rfactor 0.200
    Waters 66 Solvent Content 57.97

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The BF2203 gene from Bacteroides fragilis encodes the YP_211880 amino acid sequence of a novel secreted protein with unknown function. The protein folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). The possibility of membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. There are only a few close sequence homlogs. However, PSI-BLAST detects lots of distant homologs. Analysis sequence conservation suggests that an area near Glu172/Trp206 are potentially interesting. These two residues are also conserved in Dali hit 2in5 (hypothetical lipoprotein classified as a new fold YmcC-like in pre-SCOP) despite large structural differences, suggesting similarity in function. Thus, 3fzx likely represents a large diverse family of (lipo?)proteins with a similar function.

    Dali Hits

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  2qom-B  9.9  3.6  166   268   10 PDB  MOLECULE: SERINE PROTEASE ESPP;                                      
       2:  2qom-A  9.9  3.5  164   265   10 PDB  MOLECULE: SERINE PROTEASE ESPP;                                      
       3:  1uyn-X  9.1  4.0  163   279    8 PDB  MOLECULE: NALP;                                                      
       4:  1uyo-X  8.6  4.1  162   277    9 PDB  MOLECULE: NALP;                                                      
       5:  2in5-B  8.2  3.8  132   188   12 PDB  MOLECULE: HYPOTHETICAL LIPOPROTEIN YMCC;                             
       6:  2in5-A  8.0  4.2  137   195   11 PDB  MOLECULE: HYPOTHETICAL LIPOPROTEIN YMCC;                             
       7:  2yzy-A  7.7  3.5  118   163    8 PDB  MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN THA1012;                 
       8:  1lsh-A  7.5  3.6  142   955    8 PDB  MOLECULE: LIPOVITELLIN (LV-1N, LV-1C);                               
       9:  2v42-B  7.4  4.0  120   278    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      10:  2p4b-B  7.4  4.2  120   260    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      11:  2p4b-C  7.3  4.1  120   260    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      12:  2p4b-A  7.3  4.1  120   284    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      13:  2v43-A  7.0  4.0  121   263    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      14:  2v42-A  6.8  3.8  122   290    7 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      15:  2zf3-F  6.5  4.4  121   181    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      16:  2zf3-D  6.5  4.3  117   185    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      17:  2fr2-A  6.4  3.4  116   161    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN RV2717C;                              
      18:  2zf4-A  6.4  4.4  117   187    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      19:  3bmz-A  6.4  4.2  113   185    9 PDB  MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN;                          
      20:  2q4n-A  6.3  3.4  113   153    5 PDB  MOLECULE: UNCHARACTERIZED PROTEIN AT1G79260;                         
      21:  2zf4-B  6.2  4.2  117   180    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      22:  2zf4-C  6.2  4.3  117   181    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      23:  2zf3-E  6.2  4.4  117   186    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      24:  3emm-A  6.2  3.4  113   153    5 PDB  MOLECULE: UNCHARACTERIZED PROTEIN AT1G79260;                         
      25:  1tlz-B  6.1  3.9  135   248    7 PDB  MOLECULE: NUCLEOSIDE-SPECIFIC CHANNEL-FORMING PROTEIN TSX;           
      26:  2zf4-F  6.1  4.1  121   183    8 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      27:  2zf4-D  6.1  4.7  116   179    8 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      28:  2r4o-B  6.1  4.2  138   421    4 PDB  MOLECULE: LONG-CHAIN FATTY ACID TRANSPORT PROTEIN;                   
      29:  2v43-C  6.0  4.1  120   276    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      30:  2zf3-A  6.0  4.3  117   186    9 PDB  MOLECULE: HYPOTHETICAL PROTEIN VIOE;                                 
      31:  2byo-A  5.9  3.7  108   183   11 PDB  MOLECULE: LIPOPROTEIN LPPX;                                          
      32:  2v43-B  5.9  4.1  120   278    9 PDB  MOLECULE: SIGMA-E FACTOR REGULATORY PROTEIN RSEB;                    
      33:  3bs0-B  5.9  4.5  136   414    5 PDB  MOLECULE: TODX;    

     

    Figure 1. Structure of 3fzx.

    GS13775a.png

     

    By Piotr Kozbial [kozbial.net]:

    This putative exported protein with YmcC-like fold has predicted (LipoP server) signal peptide SpI cleavage site AGAMA|QNQDC. Phobius server predicts non-cytoplasmic localization for amino acids 21-236.

    There are two known orthologs of BF2203 protein  (CAH07951 from Bacteroides fragilis NCTC 9343 and BAD48950 from Bacteroides fragilis YCH46) and one homolog (ABR44757 from Parabacteroides distasonis ATCC 8503).

    Genome context analysis provides a weak hit (score 0.55), based on neighbourhood, with gene glyA, a serine hydroxymethyltransferase (BF2258).

     

    This is the first structural template for a new protein family of at least 70 proteins including several homologs in human gut microbiome and in metagenomic datasets. Interestingly it has 7 homologues in Gemmata obscuriglobus - a freshwater bacterium with several interesting biological features.

    Ligand Summary


     

    Two Ca ions from crystallization buffer.

    Reviews

    References

     

    No references found.

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