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The Open Protein Structure Annotation Network
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3g6i

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

    Title Crystal structure of outer membrane protein, part of carbohydrate binding complex (NP_809935.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.93 A resolution. To be published
    Site JCSG
    PDB Id 3g6i Target Id 393061
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20297,NP_809935.1, 324990 Molecular Weight 23002.87 Da.
    Residues 203 Isoelectric Point 7.00
    Sequence avdlnkenrdpkyvesivnrsqkivdklgltdakvaedvcnvianryfelndiyeirdakvkavkesgl tgdaknealkaaenekdaalyrshfafpaslslflneeqieavkdgmtygvvkvtyeatldmipslkee ekvqiyawlvearefamdaensnkkhaafgkykgrinnylakrgynltkereewakrvkarggtl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.93 Rfree 0.223
    Matthews' coefficent 3.85 Rfactor 0.197
    Waters 238 Solvent Content 68.09

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     

    Bacteriodes thetaiotaomicron BT_1022 gene encodes a secreted all-alpha protein which belongs to a small (15 members + 3 metagenome ORFs), unclassified protein family found mostly in human gut symbionts from the Bacteroides class, but also diverse marine (Blastopirellula marina) and soil (Solibacter usitatus) bacteria. Proteins from this family exist in two forms: as a short, single domain protein (eg. BT_1022) or as a domain in a larger protein (eg. BT_1017). The first form is usually a genomic neighbor of pectate lyase (BT_1023) and part of SusC/SusD containing polisaccharide utilization loci (PUL), the second follows a (putative) xylan esterase domain. For instance BT_1022 appears to be a part of a variant of SusC/SusD containing PUL (polysaccharide utilization loci). Proteins from PULs are thought to form tight complexes. The BT_1022/BT_1023/BT_1024/BT_1025 PUL could consist of SusC/SusD-like pair, pectate lyase and BT_1022 (function unknown) .

     

    3g6i structure has some similarities to other proteins (see Dali results below), but it is not clear how much these similarities reflect possible distant homologies (and resulting functional similarities) and how much they reflect structural features of 3g6i, which consists of a three-helical bundle and a long helical hairpin. 3g6i was solved as a dimer, but its it not clear if it functions as a dimer in vivo.

     

    Related target: 393277, Pfam ID DUF3826/PF12875.

     

    Figure 1. 3g6i monomer structure

     GS14013a-mono.png

     

    Figure 2. 3g6i dimer conformation

    GS14013a-dimer.png

     

     

    DALI results:

    # Query: mol1A
    # No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  2cwe-A  8.2  5.4   95   191   13   MOLECULE: HYPOTHETICAL TRANSCRIPTION REGULATOR PROTEIN,              
       2:  2d4c-B  7.1  3.4   86   231   15   MOLECULE: SH3-CONTAINING GRB2-LIKE PROTEIN 2;                        
       3:  2j68-A  6.9  3.9   95   680    6   MOLECULE: BACTERIAL DYNAMIN-LIKE PROTEIN;                            
       4:  1ek8-A  6.8  2.5   76   185   14   MOLECULE: RIBOSOME RECYCLING FACTOR;                                 
       5:  1dd5-A  6.6  4.8   80   184   15   MOLECULE: RIBOSOME RECYCLING FACTOR;                                 
       6:  1eh1-A  6.5  2.7   76   185   17   MOLECULE: RIBOSOME RECYCLING FACTOR;                                 
       7:  1uru-A  6.4  4.5   94   217    5   MOLECULE: AMPHIPHYSIN;                                               
       8:  1wqg-A  6.3  2.9   76   184   13   MOLECULE: RIBOSOME RECYCLING FACTOR;                                 
       9:  2fic-B  6.3  4.2   91   201    5   MOLECULE: BRIDGING INTEGRATOR 1;                                     
      10:  2osz-A  6.3  2.3   72    86    6   MOLECULE: NUCLEOPORIN P58/P45;                                       
      11:  2z0v-A  6.2  3.6   86   223    9   MOLECULE: SH3-CONTAINING GRB2-LIKE PROTEIN 3;                        
      12:  1y69-8  6.2  5.0   80   113   14   MOLECULE: 23S RIBOSOMAL RNA;                                         
      13:  2raj-A  6.1  3.9   92   382    2   MOLECULE: SORTING NEXIN-9;                                           
      14:  1u2m-C  6.1  3.7   75   143   13   MOLECULE: HISTONE-LIKE PROTEIN HLP-1;                                
      15:  1sxj-D  6.1  4.1   62   328   15   MOLECULE: ACTIVATOR 1 95 KDA SUBUNIT;                                
      16:  3epv-A  5.9  3.2   78   109   14   MOLECULE: NICKEL AND COBALT RESISTANCE PROTEIN CNRR;                 
      17:  2dq2-A  5.9  5.1   87   448    9   MOLECULE: SERYL-TRNA SYNTHETASE;                                     
      18:  1t7s-A  5.9  5.4   76   129   11   MOLECULE: BAG-1 COCHAPERONE;                                         
      19:  2pms-C  5.8  6.3   83   109   13   MOLECULE: LACTOTRANSFERRIN;                                          
      20:  1taz-A  5.8  7.4   76   322    7   MOLECULE: CALCIUM/CALMODULIN-DEPENDENT 3',5'-CYCLIC                  
      21:  1k30-A  5.8  3.1   65   363    6   MOLECULE: GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE;                      
      22:  1ge9-A  5.7  4.6   80   184   15   MOLECULE: RIBOSOME RECYCLING FACTOR;                                 
      23:  2v0o-A  5.7  4.1   91   273    9   MOLECULE: FCH DOMAIN ONLY PROTEIN 2;                                 
      24:  1rq0-A  5.7  5.0   74   319    8   MOLECULE: PEPTIDE CHAIN RELEASE FACTOR 1;                            
      25:  2gts-A  5.7  4.7   72    77    8   MOLECULE: HYPOTHETICAL PROTEIN HP0062;                               
      26:  1gqe-A  5.6  7.0   85   362    8   MOLECULE: RELEASE FACTOR 2;                                          
      27:  2dq3-A  5.6  5.3   89   425   11   MOLECULE: SERYL-TRNA SYNTHETASE;                                     
      28:  1wa8-A  5.6  4.9   74    99   15   MOLECULE: ESAT-6 LIKE PROTEIN ESXB;                                  
      29:  1rp3-A  5.5  6.4   85   235    8   MOLECULE: RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA);               
      30:  2ieq-B  5.5  3.1   68    89    9   MOLECULE: SPIKE GLYCOPROTEIN;                                        

     

    By Piotr Kozbial:

     

    GS14013A_alignment.png

    Figure: Multiple sequence alignment of NP_809935 with selected homologs.

     

    GS14014A_conserved-sideB.pngGS14013A_conserved-sideA.png

    Figure: Conservation pattern (calculated with ConSurf server) is shown on both sides of 3g6i protein surface. The conserved residues are: Ala20, Leu23, Val33, Arg39, Ile43, Val44, Leu47, Val58, Ile62, Ala63, Leu69, Ile72, Arg76, Asp77, Lys84, Asp105, His112, Leu119, Ser120, Ile128, Val131, Lys132, Asp133, Met135, Thr136, Val142, Asp149, Met150, Pro152, Leu154, Ile162, Glu168, Ala169, Arg170, Glu171, Met174, Asp175, His183, Phe186, Lys188, Tyr189, Gly191, Arg192, Ile193, Asn194, Asn195, Tyr196, Leu197, Lys199, Gly201, Tyr202, Asn203, Leu204, Lys206, and Arg214.
     

    Figure: 3g6i display distinctive electrostatic features

    3g6i-elec.png

     

    The N-terminus of this protein is likely to encode a signal peptide and is not present in the crystal structure. The LipPred server predicts it as non-lipoprotein with signal peptide cleavage site at position 13 (of protein precursor sequence as in GenBank: NP_809935.1).

     

    Homologous protein Fjoh_4092 from Flavobacterium johnsoniae has similar pattern of co-occurrance as: Fjoh_4093, Fjoh_4091, Fjoh_4095 (TonB-dependent receptor, plug precursor), Fjoh_4084, Fjoh_4087, Fjoh_4075 (glycoside hydrolase family 2, sugar binding precursor), Fjoh_3873, Fjoh_4105 (alpha-L-rhamnosidase precursor), Fjoh_4228 (glycoside hydrolase, family 28 precursor), and Fjoh_4435.

    BVU_2916, a homolog of BT_1022 from Bacteroides vulgatus ATCC 8482 has predicted functional partners:

     

    BVU_2915 (polysaccharide lyase family 1, candidate pectate lyase), BVU_291 (polysaccharide lyase family 1), BVU_2914 (putative outer membrane protein, probably involved in nutrient binding), BVU_2918, and BVU_2913 (putative outer membrne protein, probably involved in nutrient binding).

    Fjoh_4092 is annotated in KEGG database as protein with motifs present in DUF1090 and OmpH, but evidence to support this annotation is missing. The structure of OmpH-like protein is known, but the structural similarity is located within the alpha-helical part of BT_1022 and may be incidental.  

      End of Piotr Kozbial's contribution.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (8)

    FileSizeDateAttached by 
     3g6i-elec.png
    distinctive electrostatic properties
    136.4 kB20:01, 25 Feb 2009qxuActions
     GS14013a-dimer.png
    393061 dimer
    98.4 kB20:32, 2 Feb 2009qxuActions
     GS14013a-mono.png
    393601 monomer
    67.77 kB20:37, 2 Feb 2009qxuActions
     GS14013A_aligned.doc
    Multiple Sequence Alignment
    55.5 kB05:43, 5 Feb 2009pkozbialActions
     GS14013A_alignment.png
    Alignment
    24.74 kB05:45, 5 Feb 2009pkozbialActions
     GS14013A_conserved-sideA.png
    Conservation pattern
    289.73 kB05:45, 5 Feb 2009pkozbialActions
     GS14013A_ConSurf.pse
    Conserved-residues-are-highlighted-by-red
    665.94 kB05:44, 5 Feb 2009pkozbialActions
     GS14014A_conserved-sideB.png
    Conservation Pattern (rotated 180o). Conserved in red.
    303.12 kB05:47, 5 Feb 2009pkozbialActions
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