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Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata): The first X-ray study of an α-parvalbumin
Roquet, F.; Declercq, J.-P.; Tinant, B.; Rambaud, J.; Parello, J. (1992). Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata): The first X-ray study of an α-parvalbumin. J. Mol. Biol. 223(3): 705-720. dx.doi.org/10.1016/0022-2836(92)90985-S
In: Journal of Molecular Biology. Elsevier: London; New York. ISSN 0022-2836, more
Peer reviewed article  

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Keyword
    Marine
Author keywords
    PARVALBUMIN; CA-BINDING PROTEIN; MOLECULAR REPLACEMENT; SIMULATEDANNEALING; PROTEIN PHYLOGENY

Authors  Top 
  • Roquet, F.
  • Declercq, J.-P.
  • Tinant, B.
  • Rambaud, J.
  • Parello, J.

Abstract
    The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (α-series) is described at 1.54 Å resolution. Crystals were grown at 20 °C from 2.9 m-potassium/sodium phosphate solutions at pH5.6. The space group is P3121 and unit cell dimensions are a = b = 32.12 Å and c = 149.0 Å. The structure has been solved by the molecular replacement method using pike 4.10 parvalbumin as a model. The final structure refinement resulted in an R-factor of 17.3% for 11,363 independent reflections at 1.54 Å resolution. The shark parvalbumin shows the main features of all parvalbumins: the folding of the chain including six α-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic core.
    Compared to the structure of β-parvalbumins from pike and carp, one main difference is observed: the chain is one residue longer and this additional residue, which extends the F helix, is involved through its C-terminal carboxylate group in a network of electrostatic contacts with two basic residues, His31 in the B helix and Lys36 in the BC segment. Furthermore, hydrogen bonds exist between the side-chains of Gln108 (F helix) and Tyr26 (B helix). There is therefore a “locking” of the tertiary structure through contacts between two sequentially distant regions in the protein and this is likely to contribute to making the stability of an α-parvalbumin higher in comparison to that of a β-parvalbumin. The lengthening of the C-terminal F helix by one residue appears to be a major feature of α-parvalbumins in general, owing to the homologies of the amino acid sequences. Besides the lengthening of the C-terminal helix, the classification of the leopard shark parvalbumin in the α-series rests upon the observation of Lys13, Leu32, Glu61 and Val66.
    As this is the first crystal structure description of a parvalbumin from the α-phylogenetic lineage, it was hoped that it would clearly determine the presence or absence of a third cation binding site in parvalbumins belonging to the α-lineage. In β-pike pI 4.10 parvalbumin, Asp61 participates as a direct ligand of a third site, the satellite of the CD site. In shark parvalbumin, as in nearly all α-parvalbumins, one finds Glu at position 61. Unfortunately, the conformation of the polar head of Glu61 cannot be inferred from the X-ray data. Nevertheless, the absence of density suggests that this side-chain is not participating in any coherent co-ordination of an additional cation. On the other hand, we observe an ordered water molecule in contact with the carboxylate groups of Asp53 and Glu59, which are ligands of the third site of a typical β-parvalbumin. So, this analysis cannot unequivocally resolve whether there is a third cation binding site in α-parvalbumins.

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