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PDBsum entry 4cln
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Calcium binding protein PDB id
4cln

 

 

 

 

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Contents
Protein chain
148 a.a. *
Metals
_CA ×4
Waters ×78
* Residue conservation analysis
PDB id:
4cln
Name: Calcium binding protein
Title: Structure of a recombinant calmodulin from drosophila melanogaster refined at 2.2-angstroms resolution
Structure: Calmodulin. Chain: a. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227
Resolution:
2.20Å     R-factor:   0.197    
Authors: D.A.Taylor,J.S.Sack,J.F.Maune,K.Beckingham,F.A.Quiocho
Key ref: D.A.Taylor et al. (1991). Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-A resolution. J Biol Chem, 266, 21375-21380. PubMed id: 1939171
Date:
24-Jun-91     Release date:   15-Jul-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62152  (CALM_DROME) -  Calmodulin from Drosophila melanogaster
Seq:
Struc: 		149 a.a.
148 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
J Biol Chem 266:21375-21380 (1991)
PubMed id: 1939171  
 
 
Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-A resolution.
D.A.Taylor, J.S.Sack, J.F.Maune, K.Beckingham, F.A.Quiocho.
 
  ABSTRACT  
 
The crystal structure of calmodulin (Mr 16,700, 148 residues) from Drosophila melanogaster as expressed in a bacterial system has been determined and refined at 2.2-A resolution. Starting with the structure of mammalian calmodulin, we produced an extensively refitted and refined model with a conventional crystallographic R value of 0.197 for the 5,239 reflections (F greater than or equal to 2 sigma (F)) within the 10.0-2.2-A resolution range. The model includes 1,164 protein atoms, 4 calcium ions, and 78 water molecules and has root mean square deviations from standard values of 0.018 A for bond lengths and 0.043 A for angle distances. The overall structure is similar to mammalian calmodulin, with a seven-turn central helix connecting the two calcium-binding domains. The "dumb-bell" shaped molecule contains seven alpha-helices and four "EF hand" calcium-binding sites. Although the amino acid sequences of mammalian and Drosophila calmodulins differ by only three conservative amino acid changes, the refined model reveals a number of significant differences between the two structures. Superimposition of the structures yields a root mean square deviation of 1.22 A for the 1,120 equivalent atoms. The calcium-binding domains have a root mean square deviation of 0.85 A for the 353 equivalent atoms. There are also differences in the amino terminus, the bend of the central alpha-helix, and the orientations of some of the side chains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19391622 S.H.Bae, H.J.Dyson, and P.E.Wright (2009).
Prediction of the rotational tumbling time for proteins with disordered segments.
  J Am Chem Soc, 131, 6814-6821.  
17610210 N.Takemori, N.Komori, J.N.Thompson, M.T.Yamamoto, and H.Matsumoto (2007).
Novel eye-specific calmodulin methylation characterized by protein mapping in Drosophila melanogaster.
  Proteomics, 7, 2651-2658.  
17552906 S.L.Russell, N.V.McFerran, E.M.Hoey, A.Trudgett, and D.J.Timson (2007).
Characterisation of two calmodulin-like proteins from the liver fluke, Fasciola hepatica.
  Biol Chem, 388, 593-599.  
16533845 E.Project, R.Friedman, E.Nachliel, and M.Gutman (2006).
A molecular dynamics study of the effect of Ca2+ removal on calmodulin structure.
  Biophys J, 90, 3842-3850.  
16721661 K.Chen, J.Ruan, and L.A.Kurgan (2006).
Prediction of three dimensional structure of calmodulin.
  Protein J, 25, 57-70.  
16880936 X.Wang, J.S.Ellis, E.L.Lyle, P.Sundaram, and M.Thompson (2006).
Conformational chemistry of surface-attached calmodulin detected by acoustic shear wave propagation.
  Mol Biosyst, 2, 184-192.  
  16511158 C.L.Chyan, P.C.Huang, T.H.Lin, J.W.Huang, S.S.Lin, H.B.Huang, and Y.C.Chen (2005).
Purification, crystallization and preliminary crystallographic studies of a calmodulin-OLFp hybrid molecule.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 785-787.  
16322577 V.A.Likic, P.R.Gooley, T.P.Speed, and E.E.Strehler (2005).
A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics.
  Protein Sci, 14, 2955-2963.  
15608373 W.T.Heller (2005).
Influence of multiple well defined conformations on small-angle scattering of proteins in solution.
  Acta Crystallogr D Biol Crystallogr, 61, 33-44.  
15498938 A.G.Turjanski, D.A.Estrin, R.E.Rosenstein, J.E.McCormick, S.R.Martin, A.Pastore, R.R.Biekofsky, and V.Martorana (2004).
NMR and molecular dynamics studies of the interaction of melatonin with calmodulin.
  Protein Sci, 13, 2925-2938.  
15557269 B.Wang, S.R.Martin, R.A.Newman, S.L.Hamilton, M.A.Shea, P.M.Bayley, and K.M.Beckingham (2004).
Biochemical properties of V91G calmodulin: A calmodulin point mutation that deregulates muscle contraction in Drosophila.
  Protein Sci, 13, 3285-3297.  
15213382 C.H.Yun, J.Bai, D.Y.Sun, D.F.Cui, W.R.Chang, and D.C.Liang (2004).
Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.
  Acta Crystallogr D Biol Crystallogr, 60, 1214-1219.
PDB code: 1rfj
12972554 D.M.Casey, K.Inaba, G.J.Pazour, S.Takada, K.Wakabayashi, C.G.Wilkerson, R.Kamiya, and G.B.Witman (2003).
DC3, the 21-kDa subunit of the outer dynein arm-docking complex (ODA-DC), is a novel EF-hand protein important for assembly of both the outer arm and the ODA-DC.
  Mol Biol Cell, 14, 3650-3663.  
14635136 J.Symersky, G.Lin, S.Li, S.Qiu, M.Carson, N.Schormann, and M.Luo (2003).
Structural genomics of caenorhabditis elegans: crystal structure of calmodulin.
  Proteins, 53, 947-949.
PDB code: 1ooj
14690449 M.M.Zhu, D.L.Rempel, J.Zhao, D.E.Giblin, and M.L.Gross (2003).
Probing Ca2+-induced conformational changes in porcine calmodulin by H/D exchange and ESI-MS: effect of cations and ionic strength.
  Biochemistry, 42, 15388-15397.  
11514666 W.S.VanScyoc, and M.A.Shea (2001).
Phenylalanine fluorescence studies of calcium binding to N-domain fragments of Paramecium calmodulin mutants show increased calcium affinity correlates with increased disorder.
  Protein Sci, 10, 1758-1768.  
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.  
10024021 J.V.Lehtonen, K.Denessiouk, A.C.May, and M.S.Johnson (1999).
Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
  Proteins, 34, 341-355.  
10439509 O.Nemirovskiy, D.E.Giblin, and M.L.Gross (1999).
Electrospray ionization mass spectrometry and hydrogen/deuterium exchange for probing the interaction of calmodulin with calcium.
  J Am Soc Mass Spectrom, 10, 711-718.  
  9828012 A.L.Hazard, S.C.Kohout, N.L.Stricker, J.A.Putkey, and J.J.Falke (1998).
The kinetic cycle of cardiac troponin C: calcium binding and dissociation at site II trigger slow conformational rearrangements.
  Protein Sci, 7, 2451-2459.  
9799490 B.G.Vertessy, V.Harmat, Z.Böcskei, G.Náray-Szabó, F.Orosz, and J.Ovádi (1998).
Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies.
  Biochemistry, 37, 15300-15310.
PDB code: 1a29
  9521102 M.R.Nelson, and W.J.Chazin (1998).
An interaction-based analysis of calcium-induced conformational changes in Ca2+ sensor proteins.
  Protein Sci, 7, 270-282.  
9037719 A.R.Khan, K.A.Johnson, J.Braam, and M.N.James (1997).
Comparative modeling of the three-dimensional structure of the calmodulin-related TCH2 protein from Arabidopsis.
  Proteins, 27, 144-153.
PDB code: 1avj
9144798 B.G.Vertessy, Z.Böcskei, V.Harmath, G.Náray-Szabó, and J.Ovádi (1997).
Crystallization and preliminary diffraction analysis of Ca(2+)-calmodulin-drug and apocalmodulin-drug complexes.
  Proteins, 28, 131-134.  
  9409836 H.B.Nelson, R.G.Heiman, C.Bolduc, G.E.Kovalick, P.Whitley, M.Stern, and K.Beckingham (1997).
Calmodulin point mutations affect Drosophila development and behavior.
  Genetics, 147, 1783-1798.  
9195880 L.Tabernero, D.A.Taylor, R.J.Chandross, M.F.VanBerkum, A.R.Means, F.A.Quiocho, and J.S.Sack (1997).
The structure of a calmodulin mutant with a deletion in the central helix: implications for molecular recognition and protein binding.
  Structure, 5, 613-622.
PDB code: 1ahr
  9098889 O.B.Peersen, T.S.Madsen, and J.J.Falke (1997).
Intermolecular tuning of calmodulin by target peptides and proteins: differential effects on Ca2+ binding and implications for kinase activation.
  Protein Sci, 6, 794-807.  
9315874 R.Stevens-Truss, K.Beckingham, and M.A.Marletta (1997).
Calcium binding sites of calmodulin and electron transfer by neuronal nitric oxide synthase.
  Biochemistry, 36, 12337-12345.  
8968610 B.R.Sorensen, and M.A.Shea (1996).
Calcium binding decreases the stokes radius of calmodulin and mutants R74A, R90A, and R90G.
  Biophys J, 71, 3407-3420.  
8981747 J.Bruno, W.D.Horrocks, and K.Beckingham (1996).
Characterization of Eu(III) binding to a series of calmodulin binding site mutants using laser-induced Eu(III) luminescence spectroscopy.
  Biophys Chem, 63, 1.  
  8819155 P.M.Bayley, W.A.Findlay, and S.R.Martin (1996).
Target recognition by calmodulin: dissecting the kinetics and affinity of interaction using short peptide sequences.
  Protein Sci, 5, 1215-1228.  
  8868483 P.Mukherjea, J.F.Maune, and K.Beckingham (1996).
Interlobe communication in multiple calcium-binding site mutants of Drosophila calmodulin.
  Protein Sci, 5, 468-477.  
7552749 B.E.Finn, J.Evenäs, T.Drakenberg, J.P.Waltho, E.Thulin, and S.Forsén (1995).
Calcium-induced structural changes and domain autonomy in calmodulin.
  Nat Struct Biol, 2, 777-783.
PDB codes: 1cmf 1cmg
7743133 B.E.Finn, and S.Forsén (1995).
The evolving model of calmodulin structure, function and activation.
  Structure, 3, 7.  
8569745 H.J.Vogel, and M.Zhang (1995).
Protein engineering and NMR studies of calmodulin.
  Mol Cell Biochem, 149, 3.  
  7613465 J.W.Howarth, G.A.Krudy, X.Lin, J.A.Putkey, and P.R.Rosevear (1995).
An NMR and spin label study of the effects of binding calcium and troponin I inhibitory peptide to cardiac troponin C.
  Protein Sci, 4, 671-680.  
7601131 N.Tjandra, H.Kuboniwa, H.Ren, and A.Bax (1995).
Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements.
  Eur J Biochem, 230, 1014-1024.  
7608746 R.J.Zauhar (1995).
SMART: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications.
  J Comput Aided Mol Des, 9, 149-159.  
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
7922316 J.F.Head (1994).
Phototransduction. Shedding light on recoverin.
  Curr Biol, 4, 64-66.  
7899550 J.J.Falke, S.K.Drake, A.L.Hazard, and O.B.Peersen (1994).
Molecular tuning of ion binding to calcium signaling proteins.
  Q Rev Biophys, 27, 219-290.  
  8518733 C.Y.Sekharudu, and M.Sundaralingam (1993).
A model for the calmodulin-peptide complex based on the troponin C crystal packing and its similarity to the NMR structure of the calmodulin-myosin light chain kinase peptide complex.
  Protein Sci, 2, 620-625.  
8341660 M.Renner, M.A.Danielson, and J.J.Falke (1993).
Kinetic control of Ca(II) signaling: tuning the ion dissociation rates of EF-hand Ca(II) binding sites.
  Proc Natl Acad Sci U S A, 90, 6493-6497.  
8341712 S.Raghunathan, R.J.Chandross, B.P.Cheng, A.Persechini, S.E.Sobottka, and R.H.Kretsinger (1993).
The linker of des-Glu84-calmodulin is bent.
  Proc Natl Acad Sci U S A, 90, 6869-6873.
PDB code: 1deg
  8453381 S.T.Rao, S.Wu, K.A.Satyshur, K.Y.Ling, C.Kung, and M.Sundaralingam (1993).
Structure of Paramecium tetraurelia calmodulin at 1.8 A resolution.
  Protein Sci, 2, 436-447.
PDB code: 1clm
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.

 

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