PDBsum entry 2qvk

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protein links
Metal binding protein PDB id
Protein chain
121 a.a. *
Waters ×104
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: The second ca2+-binding domain of the na+-ca2+ exchanger is essential for regulation: crystal structures and mutational analysis
Structure: Sodium/calcium exchanger 1. Chain: a. Synonym: cbd2. Na(+)/ca(2+)-exchange protein 1. Engineered: yes
Source: Canis lupus familiaris. Dog. Organism_taxid: 9615. Strain: familiaris. Gene: slc8a1. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.45Å     R-factor:   0.163     R-free:   0.192
Authors: V.Chaptal,G.Mercado Besserer,J.Abramson,D.Cascio
Key ref:
G.M.Besserer et al. (2007). The second Ca2+-binding domain of the Na+ Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis. Proc Natl Acad Sci U S A, 104, 18467-18472. PubMed id: 17962412 DOI: 10.1073/pnas.0707417104
08-Aug-07     Release date:   13-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P23685  (NAC1_CANFA) -  Sodium/calcium exchanger 1
970 a.a.
121 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 23 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to membrane   1 term 
  Biological process     cell communication   1 term 


DOI no: 10.1073/pnas.0707417104 Proc Natl Acad Sci U S A 104:18467-18472 (2007)
PubMed id: 17962412  
The second Ca2+-binding domain of the Na+ Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis.
G.M.Besserer, M.Ottolia, D.A.Nicoll, V.Chaptal, D.Cascio, K.D.Philipson, J.Abramson.
The Na(+)-Ca(2+) exchanger plays a central role in cardiac contractility by maintaining Ca(2+) homeostasis. Two Ca(2+)-binding domains, CBD1 and CBD2, located in a large intracellular loop, regulate activity of the exchanger. Ca(2+) binding to these regulatory domains activates the transport of Ca(2+) across the plasma membrane. Previously, we solved the structure of CBD1, revealing four Ca(2+) ions arranged in a tight planar cluster. Here, we present structures of CBD2 in the Ca(2+)-bound (1.7-A resolution) and -free (1.4-A resolution) conformations. Like CBD1, CBD2 has a classical Ig fold but coordinates only two Ca(2+) ions in primary and secondary Ca(2+) sites. In the absence of Ca(2+), Lys(585) stabilizes the structure by coordinating two acidic residues (Asp(552) and Glu(648)), one from each of the Ca(2+)-binding sites, and prevents a substantial protein unfolding. We have mutated all of the acidic residues that coordinate the Ca(2+) ions and have examined the effects of these mutations on regulation of exchange activity. Three mutations (E516L, D578V, and E648L) at the primary Ca(2+) site completely remove Ca(2+) regulation, placing the exchanger into a constitutively active state. These are the first data defining the role of CBD2 as a regulatory domain in the Na(+)-Ca(2+) exchanger.
  Selected figure(s)  
Figure 2.
Fig. 2. Structure of the CBD2 Ca^2+ site. (A) The Ca^2+-binding sites of CBD2. The main chain is shown as blue ribbons. The two Ca^2+ ions and seven water molecules are depicted as green and red spheres, respectively. Primary and secondary Ca are labeled Ca1 and Ca2, respectively. Coordinating residues are displayed as a stick representation and colored by atom type (carbon, yellow; oxygen, red; nitrogen, blue). Interactions of residues with the Ca^2+ ions are represented by black dashed lines. (B) Ca^2+-free structure. Contacts (salt bridges with carboxyl residues and a hydrogen bond with a water molecule) with Lys^585 are shown with dashed black lines. The main chain is shown as yellow ribbons.
Figure 4.
Fig. 4. The mutations D552V and K585E have only modest effects on the biophysical properties of the Na^+–Ca^2+ exchanger. (A) Representative Na^+–Ca^2+ exchanger outward currents recorded from patches of oocytes expressing the indicated construct. Similar to WT, high intracellular Ca^2+ increased exchange currents and diminished the extent of Na^+-dependent inactivation of D552V and K585E. (B) Dose–response curves for cytoplasmic Ca^2+ for WT and mutant exchangers. Currents were measured at the peak amplitude. Residual current recorded in the absence of Ca^2+ has been subtracted. Each point is the average of four or five experiments.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21209335 S.A.John, B.Ribalet, J.N.Weiss, K.D.Philipson, and M.Ottolia (2011).
Ca2+-dependent structural rearrangements within Na+-Ca2+ exchanger dimers.
  Proc Natl Acad Sci U S A, 108, 1699-1704.  
20298697 C.Zamparelli, N.Macquaide, G.Colotti, D.Verzili, T.Seidler, G.L.Smith, and E.Chiancone (2010).
Activation of the cardiac Na(+)-Ca(2+) exchanger by sorcin via the interaction of the respective Ca(2+)-binding domains.
  J Mol Cell Cardiol, 49, 132-141.  
19815561 M.Wu, H.D.Le, M.Wang, V.Yurkov, A.Omelchenko, M.Hnatowich, J.Nix, L.V.Hryshko, and L.Zheng (2010).
Crystal structures of progressive Ca2+ binding states of the Ca2+ sensor Ca2+ binding domain 1 (CBD1) from the CALX Na+/Ca2+ exchanger reveal incremental conformational transitions.
  J Biol Chem, 285, 2554-2561.  
20187120 V.Breukels, and G.W.Vuister (2010).
Binding of calcium is sensed structurally and dynamically throughout the second calcium-binding domain of the sodium/calcium exchanger.
  Proteins, 78, 1813-1824.  
19243007 D.M.Bers, and S.Despa (2009).
Na(+) transport in cardiac myocytes; Implications for excitation-contraction coupling.
  IUBMB Life, 61, 215-221.  
19395557 E.Janowski, R.Day, A.Kraev, J.C.Roder, L.Cleemann, and M.Morad (2009).
beta-adrenergic regulation of a novel isoform of NCX: sequence and expression of shark heart NCX in human kidney cells.
  Am J Physiol Heart Circ Physiol, 296, H1994-H2006.  
19667209 M.Hilge, J.Aelen, A.Foarce, A.Perrakis, and G.W.Vuister (2009).
Ca2+ regulation in the Na+/Ca2+ exchanger features a dual electrostatic switch mechanism.
  Proc Natl Acad Sci U S A, 106, 14333-14338.
PDB codes: 2kls 2klt
19749753 M.Lu, J.Chai, and D.Fu (2009).
Structural basis for autoregulation of the zinc transporter YiiP.
  Nat Struct Mol Biol, 16, 1063-1067.
PDB code: 3h90
19801651 M.Ottolia, D.A.Nicoll, and K.D.Philipson (2009).
Roles of two Ca2+-binding domains in regulation of the cardiac Na+-Ca2+ exchanger.
  J Biol Chem, 284, 32735-32741.  
19622870 N.Alonso-García, A.Inglés-Prieto, A.Sonnenberg, and Pereda (2009).
Structure of the Calx-beta domain of the integrin beta4 subunit: insights into function and cation-independent stability.
  Acta Crystallogr D Biol Crystallogr, 65, 858-871.
PDB codes: 3fq4 3fso 3h6a
19332552 V.Chaptal, M.Ottolia, G.Mercado-Besserer, D.A.Nicoll, K.D.Philipson, and J.Abramson (2009).
Structure and functional analysis of a Ca2+ sensor mutant of the Na+/Ca2+ exchanger.
  J Biol Chem, 284, 14688-14692.
PDB code: 3gin
  19052365 M.Mima, C.Kawai, K.Paku, K.Tomoo, T.Ishida, S.Sugiyama, H.Matsumura, T.Kitatani, H.Y.Yoshikawa, S.Maki, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, S.Kita, and T.Iwamoto (2008).
Crystallization and preliminary X-ray crystallographic analysis of Ca2+-free primary Ca2+-sensor of Na+/Ca2+ exchanger.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1125-1127.  
18550703 Y.Xie, M.Ottolia, S.A.John, J.N.Chen, and K.D.Philipson (2008).
Conformational changes of a Ca2+-binding domain of the Na+/Ca2+ exchanger monitored by FRET in transgenic zebrafish heart.
  Am J Physiol Cell Physiol, 295, C388-C393.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.