PDBsum entry 5pal

Calcium-binding protein

PDB id: 5pal

Contents

Protein chain

109 a.a. *

Metals

_CA ×2

Waters ×92

* Residue conservation analysis

PDB id:

5pal

Name:

Calcium-binding protein

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

Structure:

Parvalbumin. Chain: a. Engineered: yes

Source:

Triakis semifasciata. Leopard shark. Organism_taxid: 30493

Resolution:

1.54Å R-factor: 0.173

Authors:

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

Key ref:

F.Roquet et al. (1992). Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin. J Mol Biol, 223, 705-720. PubMed id: 1542115 DOI: 10.1016/0022-2836(92)90985-S

Date:

25-Sep-91 Release date: 31-Oct-93

Protein chain

P30563  (PRVA_TRISE) -  Parvalbumin alpha from Triakis semifasciata

Seq: 109 a.a.

Struc: 109 a.a.

DOI no: 10.1016/0022-2836(92)90985-S

J Mol Biol 223:705-720 (1992)

PubMed id: 1542115

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

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

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)

Selected figure(s)

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 223, 705-720) copyright 1992.

Figures were selected by an automated process.