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3i10

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

    Title Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution. To be Published
    Site JCSG
    PDB Id 3i10 Target Id 396197
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25873,NP_812074.1, 332891 Molecular Weight 31470.66 Da.
    Residues 277 Isoelectric Point 7.90
    Sequence hvetikntflnpksnkvlvvahrgnwrsapenstaaidsaiamkvdiveidiqktkdgqlilmhdntld rtttgkgeiknwtladikklklkdkdgkvtnyvvptleealltakgkimvnldkaydifddvyailekt etqnqvimkggqpietvkrefgsyldkvlympvidlgnkeaekiitdylkelrpaafeiiysdpknplp pkikqllfkksliwyntlwgslagnhddnlaltdpeksygylieqlgarilqtdqpaylldylrkkgwhn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.35 Rfree 0.172
    Matthews' coefficent 2.18 Rfactor 0.150
    Waters 378 Solvent Content 43.53

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3i10
    1. Structural model for phenylalkylamine binding to L-type calcium channels
    RCK Cheng, DB Tikhonov, BS Zhorov - Journal of Biological Chemistry, 2009 - ASBMB
     
    2. Validation of the detergent micelle classification for membrane protein crystals and explanation of the Matthews Graph for soluble proteins
    GE Schulz - Protein Science, 2011 - Wiley Online Library
     
    3. CHIMERIC TRUNCATED AND MUTANT VARIANT OF TISSUE PLASMINOGEN ACTIVATOR (T-PA) RESISTANT TO PLASMINOGEN ACTIVATOR INHIBITOR-1
    F Mahboudi, F Davami, S Sardari - US Patent App. 13/191,933, 2011 - Google Patents
     

    Protein Summary

    Target NP_812074.1 is a 301-residue long protein from Bacteriodes thetaiotaomicron, a gram-negative anaerobic bacteria which resides in the human intestinal tract.  The protein belongs to the glycerophosphoryl diester phosphodiesterase (GDPD) family of proteins (family PF03009, clan CL0384), enzymes which play important roles in glycerol metabolism.  Specifically, they catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol, which serve as major sources of carbon and phosphate in an organism.

    The structure of an N-terminally truncated version of NP_812074.1 (residues 25-301) was solved by the Se-MAD method to a resolution of 1.35 Angstroms and consists of a TIM-barrel domain (residues 25-78 and 130-301, orange in Figure 1a) and a smaller domain (residues 79-129, blue in Figure 1a) that has previously been termed the GDPD-insert domain (Santelli et al. 2004).  A fastSCOP search revealed that the fold of NP_812074.1 is classified as belonging to the PLC-like phosphodiesterase superfamily in the SCOP database.

     

    Figure 1.  Structure of NP_812074.1.  (a) side view showing the two structural domains: TIM-barrel domain (orange) and a smaller GDPD-insert domain (blue) and (b) top view (rotated 90 degrees from (a) about the horizontal axis) showing the canonical TIM-barrel fold (i.e., 8-stranded beta-barrel core surrounded by 8 alpha helices).  Secondary secondary structure elements are colored as follows: alpha helices (cyan), beta strands (red), and loops (magenta).

    PX4068B-domains (1).pngPX4068B-ss.png

     

    In accordance with its Pfam assignment, the best structural homologs from both DALI and SSM were indeed glycerophosphoryl diester phosphodiesterases. (Tables 1 and 2).

     

    Table 1.  DALI structural homologs of NP_812074.1.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2pz0 24.4 2.4 230 243 28 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    2 1zcc 23.5 2.8 226 240 22 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    3 2oog 23.1 2.6 234 268 24 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    4 2p76 23.0 2.6 233 267 24 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    5 1t8q 21.9 2.8 243 329 23 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE,
    6 2o55 21.8 2.6 225 254 18 PUTATIVE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    7 1ydy 21.8 2.8 242 328 23 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    8 1o1z 21.6 2.6 220 226 21 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    9 3ch0 21.5 2.9 225 272 21 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE
    10 2otd 21.2 3.0 222 245 18 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE

     

    Table 2.  SSM structural homologs of NP_812074.1.


    N PDB Q-score RMSD TITLE
    1 2pz0 0.4624 1.987 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) FROM T. TENGCONGENSIS
    2 1o1z 0.4286 2.337 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE (GDPD) (TM1621) FROM THERMOTOGA MARITIMA AT 1.60 A RESOLUTION
    3 2oog 0.4223 2.097 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM STAPHYLOCOCCUS AUREUS
    4 1zcc 0.4172 2.111 GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM AGROBACTERIUM TUMEFACIENS STR.C58
    5 2o55 0.4062 2.346 A PUTATIVE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM GALDIERIA SULPHURARIA
    6 2otd 0.3625 2.631 THE CRYSTAL STRUCTURE OF THE GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM SHIGELLA FLEXNERI 2A
    7 1v8e 0.3462 2.364 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM THERMUS THERMOPHILUS HB8
    8 1vd6 0.3448 2.429 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE COMPLEXED WITH GLYCEROL
    9 1xi3 0.2809 2.629 THIAMINE PHOSPHATE PYROPHOSPHORYLASE FROM PYROCOCCUS FURIOSUS PFU-1255191-001
    10 1yad 0.2513 2.700 STRUCTURE OF TENI FROM BACILLUS SUBTILIS

     

    Superpostion of NP_812074.1 with the GDPD from T. Tengcongensis (PDB ID 2pz0; Shi et al., 2008), the top DALI and SSM structural homolog, reveals very close similarity between the structures (Figure 2a).

    Moreover, almost all of the residues that have biochemically been shown to constitute the active site in 2pz0 are identical in NP_812074.1.  These residues include Glu-73, Asp-75, His-46, His-88, Arg-47, and Lys-147.   The only exception is Asp-146, which in 2pz0 is a Glu instead (Figure 2b).

    In structure 2pz0, a glycerol and calcium ion were bound in the active site.  The calcium ion, which is ligated by the residues corresponding to Glu-73, Asp-75, and Asp-146 in NP_812074.1 was shown to be important for enzymatic activity.   No calcium or any other metal was observed in structure NP_812074.1, and in place of the glycerol, a PEG molecule is bound instead (Figure 2b).

     

    Figure 2.  Superposition of NP_812074.1 (yellow) with 2pz0 (blue) showing (a) the overall structural similarity.  The putative active site is located in a negatively-charged cleft at the C-terminus of the TIM-barrel (red dashed circle).  (b)  The active site residues are highly conserved between NP_812074.1 and 2pz0.  2pz0 contains a glycerol and a calcium ion at this site whereas NP_812074.1 contains a PEG molecule (represented as sticks).

     

    (a)                                                                                                (b)

     PX4068B-2pz0-superpose-2.png      PX4068B-activesite.png

     

     

    The strong similarity between NP_812074.1 and GDPDs in terms of their overall topology and active site residues strongly suggest that NP_812074.1 is indeed a GDPD.  Calcium and/or glycerophosphodiester substrate analogs could perhaps be soaked into crystals of the protein to provide structures of complexes that may provide further evidence that this is indeed the case.

     

    N.B. The GDPD from T. maritima, solved by JCSG several years ago (PDB ID 1o1z, Santelli et al., 2004), is also very similar to NP_812074.1 and 2pz0 and has all of the same active site residues as those in 2pz0.

     

    References:

    Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.  Shi L, Liu JF, An XM, Liang DC.  Proteins. 2008 Jul;72(1):280-8.

    Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.  Santelli E, Schwarzenbacher R, McMullan D, Biorac T, Brinen LS, Canaves JM, Cambell J, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA.  Proteins. 2004 Jul 1;56(1):167-70.

    Ligand Summary

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    References

     

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