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The Open Protein Structure Annotation Network
PDB Keyword
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3kl7

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

    Title Crystal structure of Putative metal-dependent hydrolase (YP_001302908.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3kl7 Target Id 393086
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS24369,YP_001302908.1, 452669 Molecular Weight 24337.23 Da.
    Residues 216 Isoelectric Point 5.91
    Sequence dsfktksgkeltitfikhgslmltydnhsiqvdpvseyadyttfpkadiilithehgdhldpkaiqave ksdteiianensqkklgkgkvlkngdtdtsisymkieavpaynttpgrdkyhprhrdngyiltfdglrv yiagdtedipemkdlkdidiaflpvnqpytmtvsqaakaarmfspkilypyhygdtkigelkdalkdsg idvrirelq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.204
    Matthews' coefficent 3.06 Rfactor 0.164
    Waters 155 Solvent Content 59.80

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Protein BDI_1531 (Target DB ID 393086 , JCSG target accession ID GS0207A, GenBank accession code YP_001302908.1) is a 241-residue long protein from Parabacteroides distasonis, an anaerobic, gram-negative bacterium that is prevalent in human intestinal flora.  BDI_1531 is annotated as a putative metal-dependent hydrolase, a classification that is supported by the analysis of the solved structure.

    The structure of an N-terminally truncated version of BDI_1531 (residues 26-241), solved by the Se-Met MAD method to a resolution of 2.3 Angstroms, consists of an internal duplication (domain 1: residues 26-117; domain 2: residues 118-241) of a beta(4)-alpha-beta-alpha motif, which is typical for a SCOP metallo-hydrolase/oxidoreductase fold, such as for instance seen in beta-lactamases.  Based on a metal excitation scan, two zinc ions have been modeled at the interface of the two domains near the surface of the protein.

    BDI_1531 protein is recognized by PFAM as a sub-threshold member of the metallo-beta-lactamase (PF00753) and lactamase_B_2 (PF12706) superfamilies.  FFAS matches it also with a cAMP phosphodiesterases class-II family (PF02112).  Most likely it would form a new family in the metallo-hydrolase/oxidoreductase clan (CL0381).

     

    Figure 1.  Structure of protein BDI_1531 (a) colored from N-terminus (blue) to C-terminus (red), (b) showing domains 1 (yellow) and 2 (blue), and (c) colored by secondary structure (helices in blue, beta-strands in red, loops in magenta).  Zinc ions are represented as green spheres in all three figures.

    (a)

    GS0207A-gradient.png  

    (b)                                                                                        (c)

    GS0207A-domains.png  GS0207A-ss.png

    The putative active site, shown in Figures 2ab, consists of two zinc ions coordinated by 5 His and 2 Asp.  Each zinc is tetrahedrally coordinated -- one of the zincs by two Asp (83 and 168) and two His (84 and 215) and the other zinc by one Asp (168) and three His (79, 81, and 146).  Each zinc shares Asp-168 as one of its ligands.

    Figure 2.  (a) coordination of the zinc ions at the putative active site of protein BDI_1531, (b) view rotated by ~90 degrees about the horizontal axis.  Zinc ions are represented as green spheres.

    (a)                                                                                        (b)

    GS0207A-activesite.png   GS0207A-activesite-2.png

     

    Consistent with protein BDI_1531's annotation as a putative metal-dependent hydrolase, both structural and sequence searches by DALI and FFAS, respectively, yield metal-dependent hydrolases as top hits (Tables 1 and 2).

    Table 1.  BDI_1531 structural neighbors as assessed by DALI.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3bv6 22.4 2.2 204 353 19 METAL-DEPENDENT HYDROLASE
    2 1zkp 19.7 2.7 193 251 20 HYPOTHETICAL PROTEIN BA1088
    3 2i7t 19.3 2.4 191 404 17 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR (Mandel et al. 2006)
    4 2i7v 19.0 2.4 192 433 17 CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR (Mandel et al. 2006)
    5 3bk2 18.5 2.7 198 549 12 METAL DEPENDENT HYDROLASE (de la Sierra-Gallay et al. 2008)
    6 3bk1 18.5 2.8 199 551 12 METAL DEPENDENT HYDROLASE (de la Sierra-Gallay et al. 2008)
    7 2cbn 18.5 2.3 188 306 20 RIBONUCLEASE Z (Kostelecky et al. 2006)
    8 2fk6 18.4 2.3 187 307 20 RIBONUCLEASE Z (Li de la Sierra-Gallay et al. 2006)
    9 1y44 18.3 2.3 187 269 21 RIBONUCLEASE Z (de la Sierra-Gallay et al. 2005)
    10 3g1p 18.2 2.6 181 249 14 PROTEIN PHNP

     

    Table 2.  BDI_1531 homologs as assessed by FFAS.

    ffas.png

     

    As shown in Figure 3a, a superposition of BDI_1531 with the top five FFAS hits (PDB ids 1vjn, 3bv6, 1zkp, 1xto, and 1ww1) reveals that they all adopt the metallo-{beta}-lactamase fold.  A comparison of the active sites among these structures shows that the active sites are also very similar, the most similar to BDI_1531's being 1zkp, which is a putative ribonuclease from Bacillus anthracis (Figure 3b).  Both BDI_1531 and 1zkp contain two zinc ions, and all of the zinc ligands are the same in both structures, raising the possibility that protein BDI_1531 may be a ribonuclease as well.

    Figure 3.  (a) Superposition of protein BDI_1531 (yellow) with top FFAS hits 1vjn (red), 3bv6 (green), 1zkp (blue), 1xto (cyan), and 1ww1 (magenta) showing the overall similarity in fold.  (b) Superposition of the active sites of the same proteins, showing their close similarity.  The active sites of BDI_1531 (yellow) and 1zkp (blue) are the most similar.  Same coloring scheme as in (a).

    (a)                                                                                                    (b)

    GS0207A-superpose-ffas.png  GS0207A-superpose-activesite.png

    Ligand Summary

    There is some elongated electron density resembling a PEG molecule located directly above the zinc ions at the putative active site.  This density has been modeled as an unidentified ligand (UNL) (Figure 4).

    Figure 4.  An unidentified ligand (UNL) has been modeled at the putative active site of BDI_1531.  The UNL is represented as red spheres, and zinc ions as green spheres.  Omit Fo-Fc electron density contoured at 3 sigmas is shown as blue mesh.

    GS0207A-unl-map.png

     

    References:

    Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.  de la Sierra-Gallay IL, Pellegrini O, Condon C. Nature. 2005 Feb 10;433(7026):657-61.

    The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins.  Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W. J Bacteriol. 2006 Feb;188(4):1607-14.

    Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.  Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C. Nat Struct Mol Biol. 2006 Apr;13(4):376-7.

    Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.  Mandel CR, Kaneko S, Zhang H, Gebauer D, Vethantham V, Manley JL, Tong L.  Nature. 2006 Dec 14;444(7121):953-6.

    Structural insights into the dual activity of RNase J. de la Sierra-Gallay IL, Zig L, Jamalli A, Putzer H. Nat Struct Mol Biol. 2008 Feb;15(2):206-12.

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