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

J Mol Biol. 2007 Nov 23;374(2):517-27. doi: 10.1016/j.jmb.2007.09.048. Epub 2007 Sep 21.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenylyl Cyclases / metabolism
  • Apoproteins / chemistry
  • Apoproteins / genetics
  • Apoproteins / metabolism
  • Binding Sites
  • Calcium / pharmacology
  • Calmodulin / chemistry*
  • Calmodulin / genetics
  • Calmodulin / metabolism
  • Cross-Linking Reagents
  • Crystallization
  • Crystallography, X-Ray
  • EF Hand Motifs
  • Humans
  • Ligands
  • Membrane Microdomains
  • Models, Molecular
  • Protein Binding
  • Protein Conformation / drug effects*
  • Protein Structure, Tertiary
  • Zinc / chemistry*

Substances

  • Apoproteins
  • Calmodulin
  • Cross-Linking Reagents
  • Ligands
  • Adenylyl Cyclases
  • Zinc
  • Calcium

Associated data

  • PDB/2PQ3