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The Open Protein Structure Annotation Network
PDB Keyword
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3elg

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

    Title Crystal structure of putative periplasmic protein of unknown function (YP_001299723.1) from Bacteroides vulgatus ATCC 8482 at 1.64 A resolution. TO BE PUBLISHED
    Site JCSG
    PDB Id 3elg Target Id 390186
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS7691,YP_001299723.1, 88179 Molecular Weight 14423.70 Da.
    Residues 127 Isoelectric Point 6.98
    Sequence agdvvtrdvnklpvaaremigkhfsqtkvayikiekdlfqttsydvkladgielefnskgewleidckn ksvpstfipqaiskymkanynghktvkiernrkgyeltlenglevdfdqfggflklsd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.64 Rfree 0.209
    Matthews' coefficent 2.57 Rfactor 0.172
    Waters 350 Solvent Content 52.23

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3elg
    1. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
    D Das, RD Finn, D Carlton, MD Miller - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

     

    Gene BVU_2443 from Bacteroides vulgatus ATCC 8482 encodes the protein YP_001299723 containing two copies of the DUF2874 sequence (PF11396). B. vulgatus is one of the most predominant microorganisms in the human gut. TMHMM and SignalP predict a signal sequence for this full protein with the signal cleavage site between residues 20-21. The solved structure is the construct from amino acids 20-146 and has the signal sequence removed.

    SCOP classifies 3elg structure inside the alpha+beta class, BLIP-like fold, BT0923-like (super)family. In the 3elg crystal structure there are two molecules in each asymmetric unit, but the interface interaction suggests that the biomolecule of 3elg is a monomer as shown below. There is a strech of acidic residues across the beta-sheet.

       

    A_91826.png

    The results from NCBI Blast search can not provide a clear clue for the possible function annotation of protein YP_001299723.1 other than hypothetical protein. Dali search provides the best hit with a JCSG target (YP_001300247.1; pdb id: PDB:3due; Z=19.6; 40% seq. id.)) which is annotated as putative periplasmic protein. The superposition between two structures is shown below.

    super_GS13115A.png

    Next Dali hit is the outer surface protein A (pdb id: 2fkj, Z=5.8). As it can be observed from the superposition below, only 82 residues out of 361 are aligned.  

    super_2fkj.png

    The SSM structure comparison suggests that the 3elg structure shares similarity with the beta lactamase inhibitor protein (BLIP, pdb id: 3d4e; JCSG structure). The superposition between 3elg (green) and 3d4e (orange) structures is shown below. The N-terminal conformation of both structures is very different. Also, the loops between beta-strands in the 3elg structure are shorter than in the BLIP.

    super_3d4e.png

    A citrate molecule coming from the crystallization conditions has been modeled in the 3elg structure interacting with residues Thr60 and Asn76 from both chains.

       

    References:

     Makabe, K.,  McElheny, D.,  Tereshko, V.,  Hilyard, A.,  Gawlak, G.,  Yan, S.,
    Koide, A.,  Koide, S.   (2006) Atomic structures of peptide self-assembly
    mimics.  Proc.Natl.Acad.Sci.Usa   103: 17753-17758 

    Ligand Summary

    Reviews

    References

     

    No references found.

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