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3gzs

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

    Title Crystal structure of SusD superfamily protein (YP_213019.1) from Bacteroides fragilis NCTC 9343 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3gzs Target Id 390164
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS7680,YP_213019.1, 283089 Molecular Weight 57646.63 Da.
    Residues 514 Isoelectric Point 5.71
    Sequence sedinrnpllptkedekmdgviygaylpnleksvipigtasestepvnryqigvnlagdawagymsprd nkfngsknftnyfmyenwvnyvysfmvtdvyspwmqikrisqdegtrndeiyalaqiikiaalhrttdm fgpipysqvgkgsfkvaydsqesvyrsflkeleeavqtlddysnkskevlpafdivyngdvnkwmrfan slmlrlairvrfadaglakeyaekavkhpaglinskelaaqmgkgaglqmknplkvineeyndtrmgat iysylagyndaraavyfvknngfkavrcgiaksgdayngftrpnvheddplywmkasevcflkaegala gfdmggsagdfynagirmsfsengldnssaetylkdstrkpanytdtsngelsanapssitirwengat eeekleriitqkylaifpngqeawtewrrtgyprqivvaenktnsavligngydlggvrrlpyprteye qngenlhnaisqylggvdnaatkvwwdkksk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.09 Rfree 0.198
    Matthews' coefficent 2.15 Rfactor 0.156
    Waters 503 Solvent Content 42.73

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gzs
    1. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
    C Bakolitsa, Q Xu, CL Rife, P Abdubek - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The BF3413 gene from Bacteroides fragilis nctc 9343 encodes the YP_213019 protein, a member of a SusD/RagA family (PFAM PF07980). Proteins from this family, present in all Bacteroidetes, in most of them in large groups of paralogs, are secreted and anchored in the outer membrane, where they function as parts of the polysaccharide binding/processing unit. Bacteroides fragilis has over 80 such units/operons, all build around pairs SusC/SusD homologs, which are an invariable part of every unit, while other partners can change.This is a sixth structure from this family (fourth at JCSG), representing a group of Bacteroides fragilis specific duplications of SusC/SusD operons, and in general, a deeply rooting branch in this family which so far had no structural representative (see a SusD family overview paper in preparation "From the sea to human microbiome, evolution of carbohydrate metabolism in human gut symbionts – the SusD family" by Christian Zmasek, Kyle Ellrott, Kayo Arima and Adam Godzik).

    monomer_ribbons.png

     

    The 3gzs structure was determined at a resolution of 2.1 Angstroms using three-wavelength Se-MAD for the primary phasing in a monoclinic crystal form. The crystal structure indicates that a monomer is the biologically-significant oligomeric form. Shown above is a ribbon representation of the structure color coded so that the N-terminal end of the monomer is blue and the C-terminal end is red. Examination of the structure shows it to be primarily composed of 22 alpha-helices. There appear to be two sets of alpha-helical bundles, an N-terminal set and a C-terminal set. The C-terminal helical bundle is oriented almost perpendicular to the N-terminal helical bundle. An extensive series of loops connects the helices and forms a cap over one end of the monomer.

     

    The structure described here is quite similar to three related structures determined by JCSG. These structures are PDB ID 3cgh (Z=49), PDB ID 3ejn (Z=35), and PDB ID 3fdh (Z=31). Shown below is a superposition of the alpha-carbon polypeptide chain of 3gzs (green) with PDB ID 3cgh (light blue), PDB ID 3ejn (pink), and PDB ID 3fdh (yellow).

     

     

    overlap_jcsg_homologs.png

     

     The table below lists protein structures from the PDB that are similar to 3gzs:

     RMSD 
     (Å) 
     Seq. 
     id 
     PDB 
     entry 
    Name
    1.42  40.5%  3cgh Crystal structure of susd homolog (np_812895.1) from bacteroides thetaiotaomicron vpi-5482 at 1.70 a resolution
    1.94  29.6%  3ejn Crystal structure of susd homolog (yp_212639.1) from bacteroides fragilis nctc 9343 at 1.50 a resolution
    2.30  24.2%  3fdh Crystal structure of susd homolog (np_810946.1) from bacteriodes thetaiotaomicron vpi-5482 at 1.75 a resolution
    2.77  18.6%   3ck8 B. Thetaiotaomicron susd with beta-cyclodextrin
    2.65  18.2%  3ckc  B. Thetaiotaomicron susd
    2.78  18.2%   3ck7 B. Thetaiotaomicron susd with alpha-cyclodextrin
    2.70  18.4%  3ckb  B. Thetaiotaomicron susd with maltotriose
    2.76  18.2%  3ck9  B. Thetaiotaomicron susd with maltoheptaose
    3.58  19.2%  1fch  Crystal structure of the pts1 complexed to the tpr region of human pex5
    3.03  14.8%   1hz4 Crystal structure of transcription factor malt domain iii

     

    Shown below is the residues surrounding the putative carbohydrate binding site in 3gzs based on a comparison with the structure of PDB ID 3ckc (Z=20), the B. thetaiotaomircon SusD complexed with cyclodextrin.

     

    putative_binding_site.bmp

     

     

     Reference

    Koropatkin, N.M.,  Martens, E.C.,  Gordon, J.I.,  Smith, T.J. (2008) Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16: 1105-1115

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (5)

    FileSizeDateAttached by 
     0-0-1236554339-esp.300.png
    Sequence Alignement-PF07980 from PDB
    70.78 kB23:33, 8 Mar 2009haxelrodActions
     monomer_ribbons.png
    Ribbon representation-monomer
    256.21 kB23:43, 8 Mar 2009haxelrodActions
     overlap_jcsg_homologs.png
    Overlap JCSG homologs
    423.9 kB00:48, 9 Mar 2009haxelrodActions
     PDBsum.gif
    PDBSum secondary structure diagram
    541.31 kB23:56, 8 Mar 2009haxelrodActions
     putative_binding_site.bmp
    Putative carbohydrate binding site
    1525.93 kB00:13, 7 Apr 2009haxelrodActions
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