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The three-dimensional structure of parvalbumin from leopard shark (Triakis
semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A
resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium
phosphate solutions at pH 5.6. The space group is P3(1)21 and unit cell
dimensions are a = b = 32.12 A and c = 149.0 A. 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 A resolution. The shark parvalbumin shows the
main features of all parvalbumins: the folding of the chain including six
alpha-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic
core. Compared to the structure of beta-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 alpha-parvalbumin
higher in comparison to that of a beta-parvalbumin. The lengthening of the
C-terminal F helix by one residue appears to be a major feature of
alpha-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 alpha-series rests upon the observation
of Lys13, Leu32, Glu61 and Val66. As this is the first crystal structure
description of a parvalbumin from the alpha-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 alpha-lineage. In beta-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
alpha-parvalbumins, one finds Glu at position 61. Unfortunately, the
conformation of the polar head of Glu61 cannot be inferred from the X-ray
data.(ABSTRACT TRUNCATED AT 400 WORDS)
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