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The Open Protein Structure Annotation Network
PDB Keyword
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3hft

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

    Title Crystal structure of WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis (NP_886680.1) from BORDETELLA BRONCHISEPTICA at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3hft Target Id 392657
    Molecular Characteristics
    Source Bordetella bronchiseptica rb50
    Alias Ids TPS24351,NP_886680.1, 323928 Molecular Weight 29807.15 Da.
    Residues 256 Isoelectric Point 5.33
    Sequence magaahrlmearmrrydnkfarisdidinqpeswrgrifltfdidwaadfvlqdtidliegagvcatwf athstpllenirrnplfelgvhpnfnpllagahaegvqeildrtlelapgcvsvrshslvqatsilnmf gerrlrydcnilvpwdagivlqpwrhwtgdmvrvpylweddvaclydwefdstfdywyqpdginvldfh pihvymnteslrryedsrevhrnpvdlirwrntsagsrtflqsllarni
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.184
    Matthews' coefficent 3.30 Rfactor 0.162
    Waters 157 Solvent Content 62.73

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hft

    Protein Summary

    Pfam note: On building, this very quickly overlaps with Polysacc_deac_1 (PF01522) for which there are several known structures.

     

    BB0128 or wbmS gene (NP_886680.1) from Bordetella bronchiseptica RB50 encodes a protein consisting of 256 residues, which is part of the O-antigen biosynthesis wbm locus. WbmS is a member of a small family proteins found in Bordetella, Campylobacter and in the ocean microbiome which is distantly related Pfam family of polysaccharide deacetylases (PF01522) (FFAS score of -12.5). Analysis of wbmS genome context indicates a possible functional link (score 0.87) with the putative formyl transferase wbmR.

    Pre-SCOP classifies 3hft in the glycoside hydrolase/deacetylase superfamily, NodB-like polysaccharide deacetylase family. Both a Dali and SSM search for structure similarity show hits to metal-ion dependent deacetylases, such as 2CC0 (Z=12), 2C79 and 2W3Z (Z=11) belonging to the NodB superfamily. DALI top hits are with the uncharacterized protein 1z7a (Z=15), the allantoinase 3cl6 (Z=14), and the deacetylase 2vyo (Z=12).

    The conserved metal-ion binding site of 3hft contains a Zn ion with 40% occupancy. The presence of zinc in the current 3hft model is supported by X-ray fluorescence, binding geometry and anomalous difference Fouriers above and below the Zn absorption edge. Asp45, His91, and His126 are the highly conserved residues participating in metal coordination.  One ethylene glycol molecule from the cryoprotectant solution complexes with the Zn ion.  Slightly differing from its  homologues, 3hft carries the Glu 177 near the metal-ion binding site, which provides the H-bonding force to hold an acetate ion from the protein purification buffer in the active site and next to the ethylene glycol molecule with clear electron density to support it.  An acetate-like ligand (UNL) is modeled next to the metal binding site according to the possible biological function of this protein, a metal-ion metal-ion dependent deacetylase.  The interface interaction suggests that 3hft forms a dimer in solution. 

     

     

    392657_1.png

     

    Figure 1. The 3hft monomer carries a conserved metal-ion binding site as deacetylase.

     

    392657_3.png

     

     

    Figure 2. 3hft could function as a dimer based on interface interaction suggested by PISA.

     

    392657_4.png

     

    Figure 3. Superposition of 3hft structure (green) with its related (Ca rmsd ~3.0 Ang.) structures: 2CC0 (red; Z=12), 2C79 (cyan; Z=11) and 2W3Z (yellow; Z=11).

     

    392657_2.png

    Figure 4.   The metal-ion binding site in 3hft supports the putative functional assignment as a deacetylase belonging to NodB superfamily. One ethylene glycol (EDO) molecule coordinates with the conversed metal ion (Zn). An acetate-like ligand (UNL) is modeled next to the EDO molecule.

     

     

    References,

    1.    Taylor, E.J.,  Gloster, T.M.,  Turkenburg, J.P.,  Vincent, F.,  Brzozowski, A.M.,  Dupont, C.,  Shareck, F.,  Centeno, M.S.,  Prates, J.A.,  Puchart, V.,  Ferreira, L.M.,  Fontes, C.M.,  Biely, P.,  Davies, G.J.  (2006) “Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases.”  J.Biol.Chem.   281: 10968-10975   
     
    2.    Deng, D.M.,  Urch, J.E.,  Ten Cate, J.M.,  Rao, V.A.,  Van Aalten, D.M.F.,  Crielaard, W.  “Streptococcus mutans SMU.623c codes for a functional, metal dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin.” J. Bacteriol. 2008 Oct 31.

    3. Allen, A., and D. Maskell. 1996. The identification, cloning and mutagenesis of a genetic locus required for lipopolysaccharide biosynthesis in Bordetella pertussis. Mol. Microbiol. 19:37–52.
     
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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