PDBsum entry 2pq3

Metal binding protein

PDB id: 2pq3

Contents

Protein chain

74 a.a. *

Ligands

CAC

Metals

_ZN ×2

Waters ×129

* Residue conservation analysis

PDB id:

2pq3

Name:

Metal binding protein

Title:

N-terminal calmodulin zn-trapped intermediate

Structure:

Calmodulin. Chain: a. Synonym: cam. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: calm1, calm, cam, cam1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.30Å R-factor: 0.143 R-free: 0.192

Authors:

J.T.Warren,Q.Guo,W.J.Tang

Key ref:

J.T.Warren et al. (2007). A 1.3-A structure of zinc-bound N-terminal domain of calmodulin elucidates potential early ion-binding step. J Mol Biol, 374, 517-527. PubMed id: 17942116 DOI: 10.1016/j.jmb.2007.09.048

Date:

01-May-07 Release date: 16-Oct-07

Protein chain

P0DP29  (CALM1_RAT) -  Calmodulin-1 from Rattus norvegicus

Seq: 149 a.a.

Struc: 74 a.a.

DOI no: 10.1016/j.jmb.2007.09.048

J Mol Biol 374:517-527 (2007)

PubMed id: 17942116

A 1.3-A structure of zinc-bound N-terminal domain of calmodulin elucidates potential early ion-binding step.

J.T.Warren, Q.Guo, W.J.Tang.

ABSTRACT

Calmodulin (CaM) is a 16.8-kDa calcium-binding protein involved in calcium-signal transduction. It is the canonical member of the EF-hand family of proteins, which are characterized by a helix-loop-helix calcium-binding motif. CaM is composed of N- and C-terminal globular domains (N-CaM and C-CaM), and within each domain there are two EF-hand motifs. Upon binding calcium, CaM undergoes a significant, global conformational change involving reorientation of the four helix bundles in each of its two domains. This conformational change upon ion binding is a key component of the signal transduction and regulatory roles of CaM, yet the precise nature of this transition is still unclear. Here, we present a 1.3-A structure of zinc-bound N-terminal calmodulin (N-CaM) solved by single-wavelength anomalous diffraction phasing of a selenomethionyl N-CaM. Our zinc-bound N-CaM structure differs from previously reported CaM structures and resembles calcium-free apo-calmodulin (apo-CaM), despite the zinc binding to both EF-hand motifs. Structural comparison with calcium-free apo-CaM, calcium-loaded CaM, and a cross-linked calcium-loaded CaM suggests that our zinc-bound N-CaM reveals an intermediate step in the initiation of metal ion binding at the first EF-hand motif. Our data also suggest that metal ion coordination by two key residues in the first metal-binding site represents an initial step in the conformational transition induced by metal binding. This is followed by reordering of the N-terminal region of the helix exiting from this first binding loop. This conformational switch should be incorporated into models of either stepwise conformational transition or flexible, dynamic energetic state sampling-based transition.

Selected figure(s)

Figure 3.
Fig. 3. Structure alignment of N-CaM with N-terminal domain of the NMR structure of apo-CaM (left, 1CFD) and the X-ray structure of Ca^2+-CaM (right, 1CLL). The residues involved in ion coordination are shown as sticks and labeled. These global alignments were performed using helices A and D, and show that our structure is predominantly in the closed conformation. 1CFD and 1CLL are presented as transparent. The two helix–loop–helix EF-hand Zn^2+-binding sites are shown in different colors: EF-hand I (helices A and B), rose red; EF-hand II (helices C and D), lime green. The spheres show the two Zn^2+ ions present in these binding sites. The zinc ion in site 2 has double occupancy. There is also a cacodylate molecule present from the crystal growth buffer with arsenic shown in purple.

Figure 4.
Fig. 4. The effect of zinc ion on the activation of two bacterial adenylyl cyclase toxins, EF and CyaA, by CaM. Assays were performed at 30 °C for 10 min in the presence of 1 nM EF or CyaA with the indicated concentration of CaM either with 10 mM ZnCl[2] or 1 μM free calcium ion buffered by EGTA; data are a representative of two experiments.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 374, 517-527) copyright 2007.

Figures were selected by an automated process.