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3no3

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

    Title Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution. To be published
    Site JCSG
    PDB Id 3no3 Target Id 396624
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS27954,YP_001301802.1, 327092 Molecular Weight 27356.81 Da.
    Residues 237 Isoelectric Point 6.27
    Sequence kdntkviahrgywktegsaqnsirsleraseigaygsefdvhltadnvlvvyhdndiqgkhiqsctyde lkdlqlsngeklptleqylkrakklknirlifelkshdtpernrdaarlsvqmvkrmklakrtdyisfn mdackefirlcpksevsylngelspmelkelgftgldyhykvlqshpdwvkdckvlgmtsnvwtvddpk lmeemidmgvdfittdlpeetqkilhsraq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.89 Rfree 0.1767
    Matthews' coefficent 2.41 Rfactor 0.1500
    Waters 300 Solvent Content 48.89

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3no3
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    I have built this and find that it overlaps with our GDPD fmaily of glycerophosphodiester phosphodiesterases.

     

    Target 396624  from Parabacteroides distasonis atcc 8503(JCSG target accession code PX7607B, GenBank accession code YP_001301802.1, UniProt A6L916) is a 237-residue protein that is annotated as a [Ref].

    glycerol-3-phosphate.

    glycerophosphodiester + H2O \rightleftharpoons alcohol + sn-glycerol 3-phosphate

    The structure of an N-terminally truncated form (residues 22-258) of 396624, which was solved by the Se-MAD method to a resolution of 1.89 Angstroms, consists of a TIM-barrel domain (residues 22-64 and 105-258, purple in Figure 1a) and a smaller domain (residues 65-104, green in Figure 1a) that has previously been termed the GDPD-insert domain [Ref].  A fastSCOP search reveals that the fold of 396624 is classified as belonging to the PLC-like phosphodiesterase superfamily in the SCOP classification scheme.

    Figure 1.  Structure of 396624.  (a) side view showing the two structural domains: TIM-barrel domain (purple) and a smaller GDPD-insert domain (green) and (b) top view showing the canonical TIM-barrel fold (i.e., 8-stranded beta-barrel core surrounded by 8 alpha helices).  Alpha helices (blue), beta strands (red), and loops (yellow).

    (a)                                                                                    (b)

    PX7607B-domains.png    PX7607B-ss.png

     

    A DALI analysis reveals the top structural matches to be other GDPDs (Table 1).

    Table 1.  Top structural neighbors of target 396624 as assessed by DALI.  Structures that are superimposed with 396624 in Figures 2 and 3 are highlighted.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2pz0 30.1 2.0 227 243 30 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE [Ref]
    2 3l12 29.6 1.7 232 295 28 PUTATIVE GLYCEROPHOSPHORYL DIESTER (TOPSAN)
    3 2o55 28.2 2.0 230 254 23 PUTATIVE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    4 3ks6 28.1 2.1 227 250 19 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    5 3ks5 28.1 2.1 227 248 19 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (TOPSAN)
    6 1v8e 28.0 1.9 215 217 25 PUTATIVE GLYCEROPHOSPHORYL DIESTER
    7 1vd6 27.9 2.0 216 218 25 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    8 3ch0 27.2 2.3 226 272 23 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (TOPSAN)
    9 2otd 26.8 2.1 221 245 22 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    10 1zcc 26.8 2.4 222 240 22 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE [Ref]

     

    Superposition of target 396624 with the top two matches shows that the structures are very similar (Figure 2).

    Figure 2.  Superposition of 396624 (yellow) with top structural matches 2pz0 (blue) and 3l12 (green).  Glycerol molecules located at the active site are represented as sticks.

    PX7607B-superpose.png

    A close-up view of the active site (Figure 3) reveals the active site residues to be nearly identical between 396624 and 2pz0 and 3l12, further supporting the assignment of target 396624 as a GDPD.

    Figure 3.  Superposition of the active sites of 396624 (yellow), 2pz0 (blue), and 3l12 (green).

    PX7607B-activesite-superpose.png

    Ligand Summary

    Reviews

    References

     

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