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The Open Protein Structure Annotation Network
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4jja

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

    Title Crystal structure of a hypothetical protein (BF0379) from Bacteroides fragilis NCTC 9343 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 4jja Target Id 418281
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS75128,YP_210109.1, 326699 Molecular Weight 41910.27 Da.
    Residues 370 Isoelectric Point 9.03
    Sequence qksdviigaeqtkayfpilknkriaifsnhtgmvgnkhlldillennfnvvaifspehgfrgnadageh vsstidsktgvpilslyngkskkpseasmkkfdilivdiqdvglrfytyyismvrlmdacaeydrkili ldrpnpnghyvdgpildmkyksgvgglpipivhgmtlgelalmvngerwlpssricdvtvipcknythq tmyrlpippspnlpnmkaiylypsiclfegtpvslgrgttlpfqvyghpnmtgynynftprsipgaknp pqlnklchgvnlsnlsdeeiwkkginldylidayhnlnmgdrffrpffellvgtdyvrkmieggksade ikarwkrdverfkiqrkpyllyqdn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.30 Rfree 0.1510
    Matthews' coefficent 1.87 Rfactor 0.1189
    Waters 335 Solvent Content 34.37

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     

     

    Two domain YP_210109.1 protein(CASP target) with largely disordered portion near the N-terminus. 3 Glycerol ligands occupy the interdomain cleft. A 3 TYR motif is involved in bonds with these ligands, which additionally involve a hydrogen bond network with few charged residues. The helix which ends with this TYR cluster contains on its other end a 'YDR' motif. In FFAS server results one finds a similar arrangement of 3 TYR cluster near a 'DRY' configuration in the first hit of ribosomal L18P/L13A proteins. It is possible that these residues of the interdomain cleft of YP_210109.1 represent the functional portion of thisprotein. Despite of these similarities, FFAS server gives only very low overall score:

     

     

    -7.580 1s72_N mol:protein length:187 50S ribosomal protein L18P

    -7.070 1wva_A mol:protein length:322 Arginase 1

    -6.170 3nfk_A mol:protein length:107 Tyrosine-protein phosphatase non-receptor type

     PredictProtein does indicate however a presence of potential phosphorylation sites near the disordered sections on the N-terminus (residues 90-110). Sequence alignment shows ~40% Id with the largely uncharacterized YzbB-like protein, participating in folate biosynthesis pathway.

    Also uncertain are Dali and Profunc predictions regarding the

     

     

    1:  1v8a-A  6.9  2.7  106   254   11 PDB  MOLECULE: HYDROXYETHYLTHIAZOLE KINASE;    
    4:  3ce9-D  6.8  5.2  148   349    6 PDB  MOLECULE: GLYCEROL DEHYDROGENASE;     
    28:  2yv2-A  6.2  3.1  104   269   14 PDB  MOLECULE: SUCCINYL-COA SYNTHETASE ALPHA CHAIN;
    

    Sequence search in ProFUNC results in 3 motifs indicating the possible functional role:

     

     

    3 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs

     

    Type

    Motif

    Name

    1.

    HMMPIR

    PIRSF016719

    Uncharacterised conserved protein, UCP016719 type

    2.

    HMMPanther

    PTHR30480

    BETA-HEXOSAMINIDASE-RELATED

    3.

    HMMPfam

    PF07075x2

    DUF1343

    Structural and sequence alignement with all pdb entries using I-Tasser identified highest rmsd of 2.6-3.0A for proteins belonging to isomerases with less than 10% sequence identity. All that information is indicating some unknown function related to Dimeric β-hexosaminidases hydrolysing hexosaminides and isomerases which convert sugars.
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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