PDBsum entry 3e9u

Membrane protein

PDB id: 3e9u

Contents

Protein chain

162 a.a. *

Waters ×23

* Residue conservation analysis

PDB id:

3e9u

Name:

Membrane protein

Title:

Crystal structure of calx cbd2 domain

Structure:

Na/ca exchange protein. Chain: a. Fragment: calx cbd2. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: calx, ncx, cg5685. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.258 R-free: 0.275

Authors:

M.Wu,L.Zheng

Key ref:

M.Wu et al. (2009). Crystal structure of CBD2 from the Drosophila Na(+)/Ca(2+) exchanger: diversity of Ca(2+) regulation and its alternative splicing modification. J Mol Biol, 387, 104-112. PubMed id: 19361442 DOI: 10.1016/j.jmb.2009.01.045

Date:

23-Aug-08 Release date: 27-Jan-09

Protein chain

Q9VDG5  (Q9VDG5_DROME) -  Sodium/calcium exchanger Calx from Drosophila melanogaster

Seq: 950 a.a.

Struc: 162 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2009.01.045

J Mol Biol 387:104-112 (2009)

PubMed id: 19361442

Crystal structure of CBD2 from the Drosophila Na(+)/Ca(2+) exchanger: diversity of Ca(2+) regulation and its alternative splicing modification.

M.Wu, M.Wang, J.Nix, L.V.Hryshko, L.Zheng.

ABSTRACT

Na(+)/Ca(2+) exchangers (NCXs) promote the extrusion of intracellular Ca(2+) to terminate numerous Ca(2+)-mediated signaling processes. Ca(2+) interaction at two Ca(2+) binding domains (CBDs; CBD1 and CBD2) is important for tight regulation of the exchange activity. Diverse Ca(2+) regulatory properties have been reported with several NCX isoforms; whether the regulatory diversity of NCXs is related to structural differences of the pair of CBDs is presently unknown. Here, we reported the crystal structure of CBD2 from the Drosophila melanogaster exchanger CALX1.1. We show that the CALX1.1-CBD2 is an immunoglobulin-like structure, similar to mammalian NCX1-CBD2, but the predicted Ca(2+) interaction region of CALX1.1-CBD2 is arranged in a manner that precludes Ca(2+) binding. The carboxylate residues that coordinate two Ca(2+) in the NCX1-CBD1 structure are neutralized by two Lys residues in CALX1.1-CBD2. This structural observation was further confirmed by isothermal titration calorimetry. The CALX1.1-CBD2 structure also clearly shows the alternative splicing region forming two adjacent helices perpendicular to CBD2. Our results provide structural evidence that the diversity of Ca(2+) regulatory properties of NCX proteins can be achieved by (1) local structure rearrangement of Ca(2+) binding site to change Ca(2+) binding properties of CBD2 and (2) alternative splicing variation altering the protein domain-domain conformation to modulate the Ca(2+) regulatory behavior.

Selected figure(s)

Figure 1.
Fig. 1. Overall structure of the CBD2 domain. The CBD2 structure of CALX1.1 was superimposed on the Ca^2+-bound CBD2 structure of canine NCX1(PDB code: 2QVM). Both structures were rendered as ribbons. The NCX1 structure is colored gray and β-strands A–G of CALX1.1 have rainbow colors. The residues in the alterative splicing region of CALX1.1-CBD2 are highlighted as stick–balls.

Figure 2.
Fig. 2. Stereo view of the pseudo-Ca^2+ binding region in the CALX1.1-CBD2 structure. The structure of CALX1.1-CBD2, shown as cyan ribbons, is superimposed onto the Ca^2+-bound NCX1-CBD2, shown as wheat ribbons. The residues in the predicted Ca^2+ binding site are depicted as stick–balls; the N/O atoms are colored blue/red. Salt bridge and hydrogen bonds in CALX1.1-CBD2 are displayed as yellow broken lines. Two Ca^2+ positions from the NCX1 structure are drawn as green spheres. The residues from NCX1 are underlined and italicized.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 387, 104-112) copyright 2009.

Figures were selected by the author.