PDBsum entry 1qiv

Calcium-binding protein

PDB id: 1qiv

Contents

Protein chain

144 a.a. *

Ligands

DPD ×2

Metals

_CA ×4

* Residue conservation analysis

PDB id:

1qiv

Name:

Calcium-binding protein

Title:

Calmodulin complexed with n-(3,3,-diphenylpropyl)-n'-[1-r-(3,4-bis- butoxyphenyl)-ethyl]-propylenediamine (dpd), 1:2 complex

Structure:

Calmodulin. Chain: a

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Organ: brain. Cellular_location: cytoplasm

Resolution:

2.64Å R-factor: 0.207 R-free: 0.301

Authors:

V.Harmat,Z.S.Bocskei,B.G.Vertessy,G.Naray-Szabo,J.Ovadi

Key ref:

V.Harmat et al. (2000). A new potent calmodulin antagonist with arylalkylamine structure: crystallographic, spectroscopic and functional studies. J Mol Biol, 297, 747-755. PubMed id: 10731425 DOI: 10.1006/jmbi.2000.3607

Date:

17-Jun-99 Release date: 28-Mar-00

Protein chain

P62157  (CALM_BOVIN) -  Calmodulin from Bos taurus

Seq: 149 a.a.

Struc: 144 a.a.

DOI no: 10.1006/jmbi.2000.3607

J Mol Biol 297:747-755 (2000)

PubMed id: 10731425

A new potent calmodulin antagonist with arylalkylamine structure: crystallographic, spectroscopic and functional studies.

V.Harmat, Z.Böcskei, G.Náray-Szabó, I.Bata, A.S.Csutor, I.Hermecz, P.Arányi, B.Szabó, K.Liliom, B.G.Vértessy, J.Ovádi.

ABSTRACT

An arylalkylamine-type calmodulin antagonist, N-(3, 3-diphenylpropyl)-N'-[1-R-(3, 4-bis-butoxyphenyl)ethyl]-propylene-diamine (AAA) is presented and its complexes with calmodulin are characterized in solution and in the crystal. Near-UV circular dichroism spectra show that AAA binds to calmodulin with 2:1 stoichiometry in a Ca(2+)-dependent manner. The crystal structure with 2:1 stoichiometry is determined to 2.64 A resolution. The binding of AAA causes domain closure of calmodulin similar to that obtained with trifluoperazine. Solution and crystal data indicate that each of the two AAA molecules anchors in the hydrophobic pockets of calmodulin, overlapping with two trifluoperazine sites, i.e. at a hydrophobic pocket and an interdomain site. The two AAA molecules also interact with each other by hydrophobic forces. A competition enzymatic assay has revealed that AAA inhibits calmodulin-activated phosphodiesterase activity at two orders of magnitude lower concentration than trifluoperazine. The apparent dissociation constant of AAA to calmodulin is 18 nM, which is commensurable with that of target peptides. On the basis of the crystal structure, we propose that the high-affinity binding is mainly due to a favorable entropy term, as the AAA molecule makes multiple contacts in its complex with calmodulin.

Selected figure(s)

Figure 5.
Figure 5. Structural details of AAA binding in the crystal structure. (a) Stereo view of (2F[o] -F[c]) electron density map contoured at the 1s level around the AAA binding sites. Carbon atoms of the AAAs are colored magenta while AAAs and methionine residues are labeled. (b) Comparison of the binding sites of AAA molecules. AAA1 (left) and AAA2 (right) (lines and circles) are shown with the interacting protein residues (lines). The orientation of CaM is changed between the left and right panels by fitting backbone atoms of the two domains onto each other considering the similar fold of those. The accommodations and conformations of the two AAAs are very similar. (c) The backbone conformation of CaM colored from the N-terminal to the C-terminal from blue to red with the two bound AAA molecules. (d) Comparison of the P3[2]21 crystal structure (red) with the P1 structure (green). The conformation of AAA changes upon the domain motion of CaM. AAA2 and the interacting helices of the N-terminal domain are shown with the C^a atoms of residues 92 to 144 fitted together. The molecular surface of the C-terminal hydrophobic pocket of CaM, calculated by GRASP [Nicholls et al 1991], is shown as a chicken-wire representation (blue). The most important interactions between AAA and CaM, shown only for P3[2]21, are emphasized with yellow shaded lines. The black arrow shows the change in conformation of AAA2 following the domain motion of CaM. (a) Drawn with Bobscript v2.3 [Esnouf 1997] and (b), (c) and (d) with MOLSCRIPT v2.1 [Kraulis 1991].

Figure 6.
Figure 6. Comparison of the AAA and TFP-binding sites of CaM. The four TFP-binding sites, as found by [Vandonselaar et al 1994], are shown as shaded ellipses and labeled T1-T4. Considering the structural similarity of the two domains, two other sites (similar to T2 and T3) can be imagined, T5 and T6 (empty ellipses).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 747-755) copyright 2000.

Figures were selected by the author.