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PDBsum entry 1ak8

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protein metals links
Calcium-binding protein PDB id
1ak8
Jmol
Contents
Protein chain
76 a.a. *
Metals
_CE ×2
* Residue conservation analysis
PDB id:
1ak8
Name: Calcium-binding protein
Title: Nmr solution structure of cerium-loaded calmodulin amino- terminal domain (ce2-tr1c), 23 structures
Structure: Calmodulin. Chain: a. Fragment: n-terminal domain, tr1c. Synonym: calmodulin cerium tr1c-domain, residues 1 - 75. Engineered: yes. Other_details: cerium-loaded n-terminal domain of vertebrate calmodulin
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: testis. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 23 models
Authors: D.Bentrop,I.Bertini,M.A.Cremonini,S.Forsen,C.Luchinat, A.Malmendal
Key ref:
D.Bentrop et al. (1997). Solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ ions by 1H NMR. Biochemistry, 36, 11605-11618. PubMed id: 9305950 DOI: 10.1021/bi971022+
Date:
29-May-97     Release date:   17-Sep-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62157  (CALM_BOVIN) -  Calmodulin
Seq:
Struc:
149 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     calcium ion binding     1 term  

 

 
DOI no: 10.1021/bi971022+ Biochemistry 36:11605-11618 (1997)
PubMed id: 9305950  
 
 
Solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ ions by 1H NMR.
D.Bentrop, I.Bertini, M.A.Cremonini, S.Forsén, C.Luchinat, A.Malmendal.
 
  ABSTRACT  
 
The solution structure of the dicerium(III) complex of the N-terminal domain of calmodulin (Ce2-TR1C hereafter) has been solved employing paramagnetic T1 relaxation enhancements and pseudocontact shifts introduced by the Ce3+ ions, together with conventional NOE constraints. The use of pseudocontact shift constraints constitutes the first attempt to locate metal ions within a protein structure by NMR. Like calcium(II), paramagnetic cerium(III) has been found to bind to the two metal binding sites of the TR1C fragment of calmodulin in a cooperative manner. Due to the presence of pseudocontact interactions between the Ce3+ ions and protons of the 76-residue protein, the 1H NMR spectra of the complex show resonances shifted between +22 and -9 ppm. Eighty percent of its proton resonances could be assigned through a standard approach using TOCSY/COSY and NOESY spectra and through 1D NOE difference spectra for the broad resonances of protons close to the paramagnetic ions. A family of structures was calculated by means of the torsion angle dynamics program DYANA [Güntert, P., Mumenthaler, C., & Wüthrich, K. (1996) XVIIthInternational Conference on Magnetic Resonance inBiological Systems (Abstract)] using 1012 NOEs. Longitudinal proton relaxation times helped to roughly define the position of the metal ions within the protein. A total of 381 pseudocontact shift constraints, whose evaluation and use are critically discussed, have then been added to further refine the metal coordinates within the protein frame and to improve the structure resolution. A dramatic resolution improvement of the metal coordinates together with a sizable resolution improvement in the regions close to the paramagnetic centers, where the number of NOEs is low, is observed. The good quality of the solution structure permitted a meaningful comparison with the solid-state structure of calcium-loaded calmodulin at 1.7 A resolution [Chattopadhyaya, R., Meador, W. E., Means, A. R., & Quiocho, F. A. (1992) J. Mol. Biol. 228, 1177]. The Ce2-TR1C complex is overall more compact than the Ca form.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21241885 P.H.Keizers, and M.Ubbink (2011).
Paramagnetic tagging for protein structure and dynamics analysis.
  Prog Nucl Magn Reson Spectrosc, 58, 88-96.  
19144926 W.Li, and R.W.Aldrich (2009).
Activation of the SK potassium channel-calmodulin complex by nanomolar concentrations of terbium.
  Proc Natl Acad Sci U S A, 106, 1075-1080.  
17180551 C.Eichmüller, and N.R.Skrynnikov (2007).
Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C.
  J Biomol NMR, 37, 79-95.  
16957918 F.Capozzi, F.Casadei, and C.Luchinat (2006).
EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
  J Biol Inorg Chem, 11, 949-962.  
16428276 I.André, T.Kesvatera, B.Jönsson, and S.Linse (2006).
Salt enhances calmodulin-target interaction.
  Biophys J, 90, 2903-2910.  
16258827 K.Simon, J.Xu, C.Kim, and N.R.Skrynnikov (2005).
Estimating the accuracy of protein structures using residual dipolar couplings.
  J Biomol NMR, 33, 83-93.  
14596622 B.Jiménez, L.Poggi, and M.Piccioli (2003).
Monitoring the early steps of unfolding of dicalcium and mono-Ce3+-substituted forms of P43M calbindin D9k.
  Biochemistry, 42, 13066-13073.
PDB code: 1n65
12644701 J.T.Welch, W.R.Kearney, and S.J.Franklin (2003).
Lanthanide-binding helix-turn-helix peptides: solution structure of a designed metallonuclease.
  Proc Natl Acad Sci U S A, 100, 3725-3730.  
14501118 M.A.Wilson, and A.T.Brunger (2003).
Domain flexibility in the 1.75 A resolution structure of Pb2+-calmodulin.
  Acta Crystallogr D Biol Crystallogr, 59, 1782-1792.
PDB code: 1n0y
12770897 M.Assfalg, I.Bertini, P.Turano, A.Grant Mauk, J.R.Winkler, and H.B.Gray (2003).
15N-1H Residual dipolar coupling analysis of native and alkaline-K79A Saccharomyces cerevisiae cytochrome c.
  Biophys J, 84, 3917-3923.  
12538884 R.Kitahara, M.Kato, and Y.Taniguchi (2003).
High-pressure 1H NMR study of pressure-induced structural changes in the heme environments of metcyanomyoglobins.
  Protein Sci, 12, 207-217.  
12237467 B.J.Goodfellow, S.G.Nunes, F.Rusnak, I.Moura, C.Ascenso, J.J.Moura, B.F.Volkman, and J.L.Markley (2002).
Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts.
  Protein Sci, 11, 2464-2470.  
11325712 D.Vigil, S.C.Gallagher, J.Trewhella, and A.E.García (2001).
Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin.
  Biophys J, 80, 2082-2092.  
10672009 I.Bertini, H.J.Hartmann, T.Klein, G.Liu, C.Luchinat, and U.Weser (2000).
High resolution solution structure of the protein part of Cu7 metallothionein.
  Eur J Biochem, 267, 1008-1018.
PDB code: 1fmy
10766953 R.Oliva, L.Falcigno, G.D'Auria, M.Saviano, L.Paolillo, G.Ansanelli, and G.Zanotti (2000).
Bicyclic peptides as models of calcium binding sites: synthesis and conformation of a homodetic undecapeptide.
  Biopolymers, 53, 581-595.  
10226044 I.Bertini, and C.Luchinat (1999).
New applications of paramagnetic NMR in chemical biology.
  Curr Opin Chem Biol, 3, 145-151.  
9786904 A.Malmendal, J.Evenäs, E.Thulin, G.P.Gippert, T.Drakenberg, and S.Forsén (1998).
When size is important. Accommodation of magnesium in a calcium binding regulatory domain.
  J Biol Chem, 273, 28994-29001.  
9538000 L.Banci, I.Bertini, M.A.De la Rosa, D.Koulougliotis, J.A.Navarro, and O.Walter (1998).
Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.
  Biochemistry, 37, 4831-4843.
PDB codes: 1a2s 1ced
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.