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The Open Protein Structure Annotation Network
PDB Keyword
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4qoa

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

    Title Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution. To be published
    Site JCSG
    PDB Id 4qoa Target Id 417915
    Molecular Characteristics
    Source Bacteroides uniformis atcc 8492
    Alias Ids TPS77966,ZP_02073090.1, 323182 Molecular Weight 14541.98 Da.
    Residues 126 Isoelectric Point 7.98
    Sequence gdvitqdtkqlpltarnfinqyfskphishikieseilqtkkyevlltdrteidfdkkgnwlevdckks avpealipvpvkeyvkanfpreiitkiergrtgveielgndyslkfnkkgkfvsmdd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.75 Rfree 0.2498
    Matthews' coefficent 4.77 Rfactor 0.2150
    Waters 17 Solvent Content 74.21

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target id 417915 is a member of the DUF2874 (PF11396) Pfam family. The sequence contains two of these DUF2874 Pfam domains. The first domain is from residues from Asp 27-Leu 82. The second DUF2874 Pfam domain is from Val 88-Val 142. Shown below is a ribbons representation of the structure of the monomer of target id 417915. The monomer consists of two structural domains. The N-terminal domain consists of residues 22-54 and a C-terminal domain consists of residues 62-146. Thus, the structural domains do not entirely correspond with the Pfam domains. The structures of five other proteins determined by JCSG (PDB IDs 3elg, 3due, 3u1w, 4dsd, and 3db7) are also members of this Pfam family and show structural similarity by DALI.

     

    SP13115D_monomer.png

     

     

    EBI-PISA predicts that a biologically significant oligomerization state of target id 417915 is a dimer. Shown below is a ribbons representation of the dimer.

     

    dimer.png

     

    The protein-protein interface of the dimer consists of primarily non-polar contacts between residues on a linker region that connects the N and C-terminal domains. Shown in the table below are structures in the PDB databank similar to target id 417915. The structures including 3elg, 3db7,3due, 4poi, and 4dsd are JCSG structures.

     

     

    PDB ID DALI Z-score rmsd (Ang) length of alignment number of residues in target sequence identity (%) Description
    3elg 13.7 1.4 90 126 40 Crystal structure of a putative periplasmic protein of unknown function (bvu_2443) from bacteroides vulgatus atcc 8482 at 1.64 A resolution
    3db7 13.5 1.6 90 127 40 Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution
    3due 12.8 1.7 89 127 38 CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION [Ref]
    4poi 11.8 2.0 87 116 53 Crystal structure of a putative periplasmic protein (BACCAC_02096) from Bacteroides caccae ATCC 43185 at 2.30 A resolution
    4dsd 11.2 2.0 87 126 54 Crystal structure of a putative periplasmic protein (BACOVA_05534) from Bacteroides ovatus ATCC 8483 at 1.75 A resolution
    3pqh 6.0 3.2 57 107 16 Crystal structure of the C-terminal fragment of the bacteriophage phi92 membrane-piercing protein gp138 [Ref]
    3u1w 5.9 4.3 81 248 12 Crystal structure of a Hypothetical PERIPLASMIC PROTEIN (BDI_1975) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
    4hbr 5.8 4.1 82 140 13 Crystal structure of a putative periplasmic proteins (BACEGG_01429) from Bacteroides eggerthii DSM 20697 at 2.40 A resolution
    4k61 5.7 4.3 82 138 12 Crystal structure of a hypothetical protein (BACUNI_01296) from Bacteroides uniformis ATCC 8492 at 1.70 A resolution

     


    Shown below is a superpositioning of the structure of target id 417915 (magenta) and PDB ID 3elg (cyan). The comparison shows that only a portion of the C-terminal domain on targetid 417915 shows structural similarity to 3elg. The comparisons are similar for the other JCSG targets. This comparison indicates that target id 417915 is different from other structures in the DUF2874 Pfam family in that it contains an extra N-terminal domain.

     

     

    3elg_dali_comparison.png

     

     

    A particular interesting observation is that portions of the two different polypeptide chains on the dimer are brought together to form a structure similar to the single monomers in the DUF2874 homologs. For example, the N-terminal domain on targetid 417915 consisting of residues 21-54 interacts with the C-terminal domain (residues 62-146) in the dimer. Shown below is a representation of the structure of an assembly formed in the targetid 417915 dimer that consists of residues 21-54 (green) and residues 62-146 (red) on the symmetry-related monomer.

    dimer_symmetry.png

     

    Shown below is a super-positioning of the assembly formed by the dimer of target id 417915 consisting of the N-terminal (green) and C-terminal domain(red) of the symmetry-related monomers onto the structure of the monomer of PDB ID 3elg (yellow)

     

    3elg_dimer_symmetry_overlap.png

    118 out of 126 of the residues in this 417915 assembly superimpose onto PDB ID 3elg with a DALI Z score of 20.6, an rmsd of 1.1 Angstroms.

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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