PDBsum entry 1b8l

Calcium binding protein

PDB id: 1b8l

Contents

Protein chain

108 a.a. *

Ligands

CO3

Metals

_CA

Waters ×159

* Residue conservation analysis

PDB id:

1b8l

Name:

Calcium binding protein

Title:

Calcium-bound d51a/e101d/f102w triple mutant of beta carp parvalbumin

Structure:

Protein (parvalbumin). Chain: a. Engineered: yes. Mutation: yes

Source:

Cyprinus carpio. Common carp. Organism_taxid: 7962. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.167 R-free: 0.227

Authors:

M.S.Cates,M.B.Berry,E.Ho,Q.Li,J.D.Potter,G.N.Phillips Jr.

Key ref:

M.S.Cates et al. (1999). Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin. Structure Fold Des, 7, 1269-1278. PubMed id: 10545326 DOI: 10.1016/S0969-2126(00)80060-X

Date:

01-Feb-99 Release date: 05-Oct-99

Protein chain

P02618  (PRVB_CYPCA) -  Parvalbumin beta from Cyprinus carpio

Seq: 108 a.a.

Struc: 108 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1016/S0969-2126(00)80060-X

Structure Fold Des 7:1269-1278 (1999)

PubMed id: 10545326

Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin.

M.S.Cates, M.B.Berry, E.L.Ho, Q.Li, J.D.Potter, G.N.Phillips.

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.

Selected figure(s)

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.

Figure was selected by an automated process.