PDBsum entry 1b8l

Calcium binding protein

PDB id: 1b8l

Contents

Protein chain

108 a.a. *

Ligands

CO3

Metals

_CA

Waters ×159

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Metal-Ion affinity and specificity in ef-Hand proteins: coordination geometry and domain plasticity in parvalbumin.
• Authors: M.S.Cates, M.B.Berry, E.L.Ho, Q.Li, J.D.Potter, G.N.Phillips.
• Ref.: Structure Fold Des, 1999, 7, 1269-1278. [DOI no: 10.1016/S0969-2126(00)80060-X]
• PubMed id: 10545326

Abstract

BACKGROUND: The EF-hand family is a large set of Ca(2+)-binding proteins that contain characteristic helix-loop-helix binding motifs that are highly conserved in sequence. Members of this family include parvalbumin and many prominent regulatory proteins such as calmodulin and troponin C. EF-hand proteins are involved in a variety of physiological processes including cell-cycle regulation, second messenger production, muscle contraction, microtubule organization and vision. RESULTS: We have determined the structures of parvalbumin mutants designed to explore the role of the last coordinating residue of the Ca(2+)-binding loop. An E101D substitution has been made in the parvalbumin EF site. The substitution decreases the Ca(2+)-binding affinity 100-fold and increases the Mg(2+)-binding affinity 10-fold. Both the Ca(2+)- and Mg(2+)-bound structures have been determined, and a structural basis has been proposed for the metal-ion-binding properties. CONCLUSIONS: The E101D mutation does not affect the Mg(2+) coordination geometry of the binding loop, but it does pull the F helix 1.1 A towards the loop. The E101D-Ca(2+) structure reveals that this mutant cannot obtain the sevenfold coordination preferred by Ca(2+), presumably because of strain limits imposed by tertiary structure. Analysis of these results relative to previously reported structural information supports a model wherein the characteristics of the last coordinating residue and the plasticity of the Ca(2+)-binding loop delimit the allowable geometries for the coordinating sphere.

Figure 3.
Figure 3. Delta distance plots of parvalbumin mutants versus wild type. (a) F102W-Ca^2+ minus wild-type carp-Ca^2+. Contours for D of ± 1 Å or greater. The absolute values of the differences in the inter-residue distances between the F102W mutant and wild type are all < 1 Å, except at the termini. The N terminus appears to be especially dynamic. (b) PVEF-Ca^2+ minus wild-type carp-Ca^2+. Contours for D of ± 1 Å or greater. The mutation at residue 51 in PVEF affects interresidue distances primarily in the CD loop (residues 51-62). There also appears to be some variation from wild-type in the C helix (residues 40-50).

The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 1269-1278) copyright 1999.

Secondary reference #1

• Title: Restrained least squares refinement of native (calcium) and cadmium-Substituted carp parvalbumin using X-Ray crystallographic data at 1.6-A resolution.
• Authors: A.L.Swain, R.H.Kretsinger, E.L.Amma.
• Ref.: J Biol Chem, 1989, 264, 16620-16628.
• PubMed id: 2777802