PDBsum entry 5pal

Calcium-binding protein

PDB id

5pal

Contents

			Protein chain

					109 a.a.

			Metals

					_CA ×2

			Waters ×92

References listed in PDB file

Key reference

Title

Crystal structure of the unique parvalbumin component from muscle of the leopard shark (triakis semifasciata). The first X-Ray study of an alpha-Parvalbumin.

Authors

F.Roquet, J.P.Declercq, B.Tinant, J.Rambaud, J.Parello.

Ref.

J Mol Biol, 1992, 223, 705-720. [DOI no: 10.1016/0022-2836(92)90985-S]

PubMed id

1542115

Abstract

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)



	Figure 2. Figure 2. istogram howing the umber f contacts < 3.40 ) etween water olecules and ain chain (filled ars) or side-chain open ars) atoms of the heliees and f the oops btween the helics.		Figure 9. Figure 9. tereo diagram f ontacts between the B-helix (Tyr26, Lys27, Hisal), the BC loop 4~~36) and the C-terminal domain F-helix: la109, ln108) (p r g am PLUTO; Motherwell legg, 978). Distances (A): la109 -T1 to is31 NE2 = 3.08; Ala109 O-T1 to Lys36 C = 253; la109 -T2 to is31 E2 = 286; Gln108 OE' to yr26 OH = 2.88.