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PDBsum entry 3pal

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protein metals links
Calcium binding protein PDB id
3pal
Jmol
Contents
Protein chain
108 a.a. *
Metals
_MG
_CA ×2
Waters ×95
* Residue conservation analysis
PDB id:
3pal
Name: Calcium binding protein
Title: Ionic interactions with parvalbumins. Crystal structure determination of pike 4.10 parvalbumin in four different ionic environments
Structure: Parvalbumin. Chain: a. Engineered: yes
Source: Esox lucius. Northern pike. Organism_taxid: 8010
Resolution:
2.40Å     R-factor:   0.167    
Authors: J.P.Declercq,B.Tinant,J.Parello,J.Rambaud
Key ref: J.P.Declercq et al. (1991). Ionic interactions with parvalbumins. Crystal structure determination of pike 4.10 parvalbumin in four different ionic environments. J Mol Biol, 220, 1017-1039. PubMed id: 1880797
Date:
08-Nov-90     Release date:   15-Jan-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02619  (PRVB_ESOLU) -  Parvalbumin beta
Seq:
Struc:
107 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     2 terms  

 

 
J Mol Biol 220:1017-1039 (1991)
PubMed id: 1880797  
 
 
Ionic interactions with parvalbumins. Crystal structure determination of pike 4.10 parvalbumin in four different ionic environments.
J.P.Declercq, B.Tinant, J.Parello, J.Rambaud.
 
  ABSTRACT  
 
The crystal structure of the Ca-loaded form of pike 4.10 parvalbumin (minor component from pike muscle belonging to the beta phylogenetic series), with both its primary sites CD and EF occupied by Ca2+ ions and its third site occupied by an ammonium ion, as previously determined at 1.93 A resolution, has now been refined to a resolution of 1.65 A. The crystallization of this parvalbumin in different ionic environments has allowed three novel non-isomorphous crystalline forms to be obtained: (1) a first form, crystallized in the presence of a mixture of ammonium sulphate and manganese sulphate, for which all the cation binding sites in the protein are occupied by Mn2+; (2) a second form crystallized in the presence of MgSO4 as the precipitating agent, only differs from the Ca/NH4 form by the occupation of the third site by Mg2+, whereas the primary sites remain occupied by Ca2+; (3) a third form, also crystallized in the presence of MgSO4, corresponds to a well-defined molecular species with both the primary EF site and the third site occupied by Mg2+, whereas the primary CD site remains occupied by CA2+. The corresponding molecular structures reported here have been determined at resolutions between 1.8 and 2.4 A. The comparison of the different crystal structures allows the structural modifications accompanying the substitution of the primary sites by cations differing significantly in their ionic radii (Ca2+, Mn2+, Mg2+) to be investigated in detail, and it also leads to a precise description of the third site in a typical beta parvalbumin. The substitution Ca2+ by Mg2+ within the primary site EF is characterized by a "contraction" of the co-ordination sphere, with a decrease of the mean oxygen-metal distance by a value of 0.25 A and a decrease of the co-ordination number from 7 to 6, as a consequence of the loss of a bidentate ligand (Glu101), which becomes a monodentate one. Such an adaptation of the co-ordination sphere around a cation of smaller size involves, among others, the transformation of the Glu101 side-chain from the stable gauche(+) form to the less stable gauche(-) form. The third site is clearly described as a satellite of the CD primary site, since both sites possess common protein ligands, such as Asp53 and Glu59. Furthermore, Asp61 appears as a specific ligand of the third site in the different environments investigated in this work. We finally discuss the relevance of the third site to parvalbumin phylogeny.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262274 Z.Grabarek (2011).
Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins.
  Biochim Biophys Acta, 1813, 913-921.  
19651438 S.E.Permyakov, A.G.Bakunts, M.E.Permyakova, A.I.Denesyuk, V.N.Uversky, and E.A.Permyakov (2009).
Metal-controlled interdomain cooperativity in parvalbumins.
  Cell Calcium, 46, 163-175.  
18260106 S.E.Permyakov, A.G.Bakunts, A.I.Denesyuk, E.L.Knyazeva, V.N.Uversky, and E.A.Permyakov (2008).
Apo-parvalbumin as an intrinsically disordered protein.
  Proteins, 72, 822-836.  
17094115 S.J.Lee, C.C.Ju, S.L.Chu, M.S.Chien, T.H.Chan, and W.L.Liao (2007).
Molecular cloning, expression and phylogenetic analyses of parvalbumin in tilapia, Oreochromis mossambicus.
  J Exp Zool Part A Ecol Genet Physiol, 307, 51-61.  
15169955 C.A.Bottoms, J.P.Schuermann, S.Agah, M.T.Henzl, and J.J.Tanner (2004).
Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.
  Protein Sci, 13, 1724-1734.
PDB code: 1rwy
11867433 M.S.Cates, M.L.Teodoro, and G.N.Phillips (2002).
Molecular mechanisms of calcium and magnesium binding to parvalbumin.
  Biophys J, 82, 1133-1146.  
11948788 W.Yang, H.W.Lee, H.Hellinga, and J.J.Yang (2002).
Structural analysis, identification, and design of calcium-binding sites in proteins.
  Proteins, 47, 344-356.  
11733025 F.Yumoto, M.Nara, H.Kagi, W.Iwasaki, T.Ojima, K.Nishita, K.Nagata, and M.Tanokura (2001).
Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups.
  Eur J Biochem, 268, 6284-6290.  
11562941 M.Thépaut, M.P.Strub, A.Cavé, J.L.Banères, M.W.Berchtold, C.Dumas, and A.Padilla (2001).
Structure of rat parvalbumin with deleted AB domain: implications for the evolution of EF hand calcium-binding proteins and possible physiological relevance.
  Proteins, 45, 117-128.
PDB code: 1g33
11258955 S.B.Tikunova, D.J.Black, J.D.Johnson, and J.P.Davis (2001).
Modifying Mg2+ binding and exchange with the N-terminal of calmodulin.
  Biochemistry, 40, 3348-3353.  
10764710 A.Bugajska-Schretter, M.Grote, L.Vangelista, P.Valent, W.R.Sperr, H.Rumpold, A.Pastore, R.Reichelt, R.Valenta, and S.Spitzauer (2000).
Purification, biochemical, and immunological characterisation of a major food allergen: different immunoglobulin E recognition of the apo- and calcium-bound forms of carp parvalbumin.
  Gut, 46, 661-669.  
11114499 A.Lewit-Bentley, and S.Réty (2000).
EF-hand calcium-binding proteins.
  Curr Opin Struct Biol, 10, 637-643.  
10757979 J.L.Enmon, T.de Beer, and M.Overduin (2000).
Solution structure of Eps15's third EH domain reveals coincident Phe-Trp and Asn-Pro-Phe binding sites.
  Biochemistry, 39, 4309-4319.
PDB code: 1c07
  10739249 R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, and D.J.Nelson (2000).
X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).
  Protein Sci, 9, 73-82.
PDB code: 1bu3
  11206069 S.R.Martin, L.Masino, and P.M.Bayley (2000).
Enhancement by Mg2+ of domain specificity in Ca2+-dependent interactions of calmodulin with target sequences.
  Protein Sci, 9, 2477-2488.  
11087403 T.Ozawa, M.Fukuda, M.Nara, A.Nakamura, Y.Komine, K.Kohama, and Y.Umezawa (2000).
How can Ca2+ selectively activate recoverin in the presence of Mg2+? Surface plasmon resonance and FT-IR spectroscopic studies.
  Biochemistry, 39, 14495-14503.  
10233057 J.M.Zanotti, M.C.Bellissent-Funel, and J.Parello (1999).
Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin.
  Biophys J, 76, 2390-2411.  
  10548066 J.P.Declercq, C.Evrard, V.Lamzin, and J.Parello (1999).
Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core.
  Protein Sci, 8, 2194-2204.
PDB code: 2pvb
10545326 M.S.Cates, M.B.Berry, E.L.Ho, Q.Li, J.D.Potter, and G.N.Phillips (1999).
Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin.
  Structure, 7, 1269-1278.
PDB codes: 1b8c 1b8l 1b8r 1b9a
10223291 S.Y.Chung, and S.Subbiah (1999).
Validation of NMR side-chain conformations by packing calculations.
  Proteins, 35, 184-194.  
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.  
9665701 C.Baldellon, J.R.Alattia, M.P.Strub, T.Pauls, M.W.Berchtold, A.Cavé, and A.Padilla (1998).
15N NMR relaxation studies of calcium-loaded parvalbumin show tight dynamics compared to those of other EF-hand proteins.
  Biochemistry, 37, 9964-9975.  
9548926 R.Gilli, D.Lafitte, C.Lopez, M.Kilhoffer, A.Makarov, C.Briand, and J.Haiech (1998).
Thermodynamic analysis of calcium and magnesium binding to calmodulin.
  Biochemistry, 37, 5450-5456.  
9585577 R.R.Biekofsky, S.R.Martin, J.P.Browne, P.M.Bayley, and J.Feeney (1998).
Ca2+ coordination to backbone carbonyl oxygen atoms in calmodulin and other EF-hand proteins: 15N chemical shifts as probes for monitoring individual-site Ca2+ coordination.
  Biochemistry, 37, 7617-7629.  
  9194174 M.Andersson, A.Malmendal, S.Linse, I.Ivarsson, S.Forsén, and L.A.Svensson (1997).
Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k.
  Protein Sci, 6, 1139-1147.
PDB codes: 1ig5 1igv 5icb 6icb
9154918 M.Laberge, W.W.Wright, K.Sudhakar, P.A.Liebman, and J.M.Vanderkooi (1997).
Conformational effects of calcium release from parvalbumin: comparison of computational simulations with spectroscopic investigations.
  Biochemistry, 36, 5363-5371.  
  9236210 S.K.Drake, M.A.Zimmer, C.Kundrot, and J.J.Falke (1997).
Molecular tuning of an EF-hand-like calcium binding loop. Contributions of the coordinating side chain at loop position 3.
  J Gen Physiol, 110, 173-184.  
  9385642 S.P.Revett, G.King, J.Shabanowitz, D.F.Hunt, K.L.Hartman, T.M.Laue, and D.J.Nelson (1997).
Characterization of a helix-loop-helix (EF hand) motif of silver hake parvalbumin isoform B.
  Protein Sci, 6, 2397-2408.
PDB code: 1bu3
8973641 I.Durussel, T.L.Pauls, J.A.Cox, and M.W.Berchtold (1996).
Chimeras of parvalbumin and oncomodulin involving exchange of the complete CD site show that the Ca2+/Mg2+ specificity is an intrinsic property of the site.
  Eur J Biochem, 242, 256-263.  
8973640 T.L.Pauls, I.Durussel, I.D.Clark, A.G.Szabo, M.W.Berchtold, and J.A.Cox (1996).
Site-specific replacement of amino acid residues in the CD site of rat parvalbumin changes the metal specificity of this Ca2+/Mg(2+)-mixed site toward a Ca(2+)-specific site.
  Eur J Biochem, 242, 249-255.  
8611623 T.L.Pauls, J.A.Cox, and M.W.Berchtold (1996).
The Ca2+(-)binding proteins parvalbumin and oncomodulin and their genes: new structural and functional findings.
  Biochim Biophys Acta, 1306, 39-54.  
7896823 A.C.da Silva, J.Kendrick-Jones, and F.C.Reinach (1995).
Determinants of ion specificity on EF-hands sites. Conversion of the Ca2+/Mg2+ site of smooth muscle myosin regulatory light chain into a Ca(2+)-specific site.
  J Biol Chem, 270, 6773-6778.  
7784428 D.W.Deerfield, D.J.Fox, M.Head-Gordon, R.G.Hiskey, and L.G.Pedersen (1995).
The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.
  Proteins, 21, 244-255.  
7636317 G.E.Searles, W.T.Dixon, P.D.Thomas, and K.Jimbow (1995).
Divalent cations control cell-substrate adhesion and laminin expression in normal and malignant human melanocytes in early and late stages of cellular differentiation.
  J Invest Dermatol, 105, 301-308.  
7551560 T.S.Lange, J.Kirchberg, A.K.Bielinsky, A.Leuker, I.Bank, T.Ruzicka, and K.Scharffetter-Kochanek (1995).
Divalent cations (Mg2+, Ca2+) differentially influence the beta 1 integrin-mediated migration of human fibroblasts and keratinocytes to different extracellular matrix proteins.
  Exp Dermatol, 4, 130-137.  
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.  
  7703855 X.L.Ding, A.B.Akella, H.Su, and J.Gulati (1994).
The role of glycine (residue 89) in the central helix of EF-hand protein troponin-C exposed following amino-terminal alpha-helix deletion.
  Protein Sci, 3, 2089-2096.  
7510713 Y.van Kooyk, P.Weder, K.Heije, and C.G.Figdor (1994).
Extracellular Ca2+ modulates leukocyte function-associated antigen-1 cell surface distribution on T lymphocytes and consequently affects cell adhesion.
  J Cell Biol, 124, 1061-1070.  
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.  
8354278 U.G.Föhr, B.R.Weber, M.Müntener, W.Staudenmann, G.J.Hughes, S.Frutiger, D.Banville, B.W.Schäfer, and C.W.Heizmann (1993).
Human alpha and beta parvalbumins. Structure and tissue-specific expression.
  Eur J Biochem, 215, 719-727.  
1374416 J.J.Grzesiak, G.E.Davis, D.Kirchhofer, and M.D.Pierschbacher (1992).
Regulation of alpha 2 beta 1-mediated fibroblast migration on type I collagen by shifts in the concentrations of extracellular Mg2+ and Ca2+.
  J Cell Biol, 117, 1109-1117.  
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.