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PDBsum entry 1la3

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protein ligands metals links
Metal-binding protein PDB id
1la3
Jmol
Contents
Protein chain
188 a.a. *
Ligands
MYR
Metals
_CA
* Residue conservation analysis
PDB id:
1la3
Name: Metal-binding protein
Title: Solution structure of recoverin mutant, e85q
Structure: Recoverin. Chain: a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: retina. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 14 models
Authors: J.B.Ames,N.Hamasaki,T.Molchanova
Key ref:
J.B.Ames et al. (2002). Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state. Biochemistry, 41, 5776-5787. PubMed id: 11980481 DOI: 10.1021/bi012153k
Date:
27-Mar-02     Release date:   19-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21457  (RECO_BOVIN) -  Recoverin
Seq:
Struc:
202 a.a.
188 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     response to stimulus   4 terms 
  Biochemical function     protein binding     3 terms  

 

 
DOI no: 10.1021/bi012153k Biochemistry 41:5776-5787 (2002)
PubMed id: 11980481  
 
 
Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state.
J.B.Ames, N.Hamasaki, T.Molchanova.
 
  ABSTRACT  
 
Recoverin, a member of the EF-hand superfamily, serves as a calcium sensor in retinal rod cells. A myristoyl or related fatty acyl group covalently attached to the N-terminus of recoverin facilitates the binding of recoverin to retinal disk membranes by a mechanism known as the Ca2+-myristoyl switch. Previous structural studies revealed that the myristoyl group of recoverin is sequestered inside the protein core in the absence of calcium. The cooperative binding of two calcium ions to the second and third EF-hands (EF-2 and EF-3) of recoverin leads to the extrusion of the fatty acid. Here we present nuclear magnetic resonance (NMR), fluorescence, and calcium-binding studies of a myristoylated recoverin mutant (myr-E85Q) designed to abolish high-affinity calcium binding to EF-2 and thereby trap the myristoylated protein with calcium bound solely to EF-3. Equilibrium calcium-binding studies confirm that only one Ca2+ binds to myr-E85Q under the conditions of this study with a dissociation constant of 100 microM. Fluorescence and NMR spectra of the Ca2+-free myr-E85Q are identical to those of Ca2+-free wild type, indicating that the E85Q mutation does not alter the stability and structure of the Ca2+-free protein. In contrast, the fluorescence and NMR spectra of half-saturated myr-E85Q (one bound Ca2+) look different from those of Ca2+-saturated wild type (two bound Ca2+), suggesting that half-saturated myr-E85Q may represent a structural intermediate. We report here the three-dimensional structure of Ca2+-bound myr-E85Q as determined by NMR spectroscopy. The N-terminal myristoyl group of Ca2+-bound myr-E85Q is sequestered within a hydrophobic cavity lined by many aromatic residues (F23, W31, Y53, F56, F83, and Y86) resembling that of Ca2+-free recoverin. The structure of Ca2+-bound myr-E85Q in the N-terminal region (residues 2-90) is similar to that of Ca2+-free recoverin, whereas the C-terminal region (residues 100-202) is more similar to that of Ca2+-bound wild type. Hence, the structure of Ca2+-bound myr-E85Q represents a hybrid between the structures of recoverin with zero and two Ca2+ bound. The binding of Ca2+ to EF-3 leads to local structural changes within the EF-hand that alter the domain interface and cause a 45 degrees swiveling of the N- and C-terminal domains, resulting in a partial unclamping of the myristoyl group. We propose that Ca2+-bound myr-E85Q may represent a stable intermediate state in the kinetic mechanism of the calcium-myristoyl switch.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21327964 S.Theisgen, L.Thomas, T.Schröder, C.Lange, M.Kovermann, J.Balbach, and D.Huster (2011).
The presence of membranes or micelles induces structural changes of the myristoylated guanylate-cyclase activating protein-2.
  Eur Biophys J, 40, 565-576.  
  21465563 X.Xu, R.Ishima, and J.B.Ames (2011).
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
  Proteins, 79, 1910-1922.  
18942727 J.L.Li, C.Y.Geng, Y.Bu, X.R.Huang, and C.C.Sun (2009).
Conformational transition pathway in the allosteric process of calcium-induced recoverin: molecular dynamics simulations.
  J Comput Chem, 30, 1135-1145.  
19143494 S.Lim, I.Peshenko, A.Dizhoor, and J.B.Ames (2009).
Effects of Ca2+, Mg2+, and myristoylation on guanylyl cyclase activating protein 1 structure and stability.
  Biochemistry, 48, 850-862.  
18485069 J.Traba, E.M.Froschauer, G.Wiesenberger, J.Satrústegui, and A.Del Arco (2008).
Yeast mitochondria import ATP through the calcium-dependent ATP-Mg/Pi carrier Sal1p, and are ATP consumers during aerobic growth in glucose.
  Mol Microbiol, 69, 570-585.  
18346093 R.Stephen, S.Filipek, K.Palczewski, and M.C.Sousa (2008).
Ca2+ -dependent regulation of phototransduction.
  Photochem Photobiol, 84, 903-910.  
18034895 I.I.Senin, V.A.Churumova, P.P.Philippov, and K.W.Koch (2007).
Membrane binding of the neuronal calcium sensor recoverin - modulatory role of the charged carboxy-terminus.
  BMC Biochem, 8, 24.  
17311005 R.D.Burgoyne (2007).
Neuronal calcium sensor proteins: generating diversity in neuronal Ca2+ signalling.
  Nat Rev Neurosci, 8, 182-193.  
17078090 T.Gensch, K.E.Komolov, I.I.Senin, P.P.Philippov, and K.W.Koch (2007).
Ca2+-dependent conformational changes in the neuronal Ca2+-sensor recoverin probed by the fluorescent dye Alexa647.
  Proteins, 66, 492-499.  
17020884 J.B.Ames, K.Levay, J.N.Wingard, J.D.Lusin, and V.Z.Slepak (2006).
Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin.
  J Biol Chem, 281, 37237-37245.
PDB code: 2i94
16432210 M.Ikura, and J.B.Ames (2006).
Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality.
  Proc Natl Acad Sci U S A, 103, 1159-1164.  
17015448 O.H.Weiergräber, I.I.Senin, E.Y.Zernii, V.A.Churumova, N.A.Kovaleva, A.A.Nazipova, S.E.Permyakov, E.A.Permyakov, P.P.Philippov, J.Granzin, and K.W.Koch (2006).
Tuning of a neuronal calcium sensor.
  J Biol Chem, 281, 37594-37602.
PDB code: 2het
16147998 J.N.Wingard, J.Chan, I.Bosanac, F.Haeseleer, K.Palczewski, M.Ikura, and J.B.Ames (2005).
Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels.
  J Biol Chem, 280, 37461-37470.  
15843174 K.E.Komolov, D.V.Zinchenko, V.A.Churumova, S.A.Vaganova, O.H.Weiergräber, I.I.Senin, P.P.Philippov, and K.W.Koch (2005).
One of the Ca2+ binding sites of recoverin exclusively controls interaction with rhodopsin kinase.
  Biol Chem, 386, 285-289.  
16148003 K.T.Buchanan, J.B.Ames, S.H.Asfaw, J.N.Wingard, C.L.Olson, P.T.Campana, A.P.Araújo, and D.M.Engman (2005).
A flagellum-specific calcium sensor.
  J Biol Chem, 280, 40104-40111.  
15746104 M.Osawa, A.Dace, K.I.Tong, A.Valiveti, M.Ikura, and J.B.Ames (2005).
Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM.
  J Biol Chem, 280, 18008-18014.  
14726528 D.W.O'Callaghan, and R.D.Burgoyne (2004).
Identification of residues that determine the absence of a Ca(2+)/myristoyl switch in neuronal calcium sensor-1.
  J Biol Chem, 279, 14347-14354.  
14722091 N.Hamasaki-Katagiri, T.Molchanova, K.Takeda, and J.B.Ames (2004).
Fission yeast homolog of neuronal calcium sensor-1 (Ncs1p) regulates sporulation and confers calcium tolerance.
  J Biol Chem, 279, 12744-12754.  
15704013 W.A.McLaughlin, D.W.Kulp, J.de la Cruz, X.J.Lu, C.L.Lawson, and H.M.Berman (2004).
A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction.
  J Struct Funct Genomics, 5, 255-265.  
12871972 M.Nagae, A.Nozawa, N.Koizumi, H.Sano, H.Hashimoto, M.Sato, and T.Shimizu (2003).
The crystal structure of the novel calcium-binding protein AtCBL2 from Arabidopsis thaliana.
  J Biol Chem, 278, 42240-42246.
PDB code: 1uhn
12686556 O.H.Weiergräber, I.I.Senin, P.P.Philippov, J.Granzin, and K.W.Koch (2003).
Impact of N-terminal myristoylation on the Ca2+-dependent conformational transition in recoverin.
  J Biol Chem, 278, 22972-22979.
PDB codes: 1omr 1omv
12393897 I.I.Senin, T.Fischer, K.E.Komolov, D.V.Zinchenko, P.P.Philippov, and K.W.Koch (2002).
Ca2+-myristoyl switch in the neuronal calcium sensor recoverin requires different functions of Ca2+-binding sites.
  J Biol Chem, 277, 50365-50372.  
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 code is shown on the right.