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PDBsum entry 5pal

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protein metals links
Calcium-binding protein PDB id
5pal
Jmol PyMol
Contents
Protein chain
109 a.a. *
Metals
_CA ×2
Waters ×92
* Residue conservation analysis
PDB id:
5pal
Name: Calcium-binding protein
Title: Crystal structure of the unique parvalbumin component from muscle of the leopard shark (triakis semifasciata). The first x-ray study of an alpha-parvalbumin
Structure: Parvalbumin. Chain: a. Engineered: yes
Source: Triakis semifasciata. Leopard shark. Organism_taxid: 30493
Resolution:
1.54Å     R-factor:   0.173    
Authors: F.Roquet,J.-P.Declercq,B.Tinant,J.Rambaud,J.Parello
Key ref:
F.Roquet et al. (1992). Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin. J Mol Biol, 223, 705-720. PubMed id: 1542115 DOI: 10.1016/0022-2836(92)90985-S
Date:
25-Sep-91     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P30563  (PRVA_TRISE) -  Parvalbumin alpha
Seq:
Struc:
109 a.a.
109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/0022-2836(92)90985-S J Mol Biol 223:705-720 (1992)
PubMed id: 1542115  
 
 
Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin.
F.Roquet, J.P.Declercq, B.Tinant, J.Rambaud, J.Parello.
 
  ABSTRACT  
 
The three-dimensional structure of parvalbumin from leopard shark (Triakis semifasciata) with 109 amino acid residues (alpha-series) is described at 1.54 A resolution. Crystals were grown at 20 degrees C from 2.9 M-potassium/sodium phosphate solutions at pH 5.6. The space group is P3(1)21 and unit cell dimensions are a = b = 32.12 A and c = 149.0 A. The structure has been solved by the molecular replacement method using pike 4.10 parvalbumin as a model. The final structure refinement resulted in an R-factor of 17.3% for 11,363 independent reflections at 1.54 A resolution. The shark parvalbumin shows the main features of all parvalbumins: the folding of the chain including six alpha-helices, the salt bridge between Arg75 and Glu81, and the hydrophobic core. Compared to the structure of beta-parvalbumins from pike and carp, one main difference is observed: the chain is one residue longer and this additional residue, which extends the F helix, is involved through its C-terminal carboxylate group in a network of electrostatic contacts with two basic residues, His31 in the B helix and Lys36 in the BC segment. Furthermore, hydrogen bonds exist between the side-chains of Gln108 (F helix) and Tyr26 (B helix). There is therefore a "locking" of the tertiary structure through contacts between two sequentially distant regions in the protein and this is likely to contribute to making the stability of an alpha-parvalbumin higher in comparison to that of a beta-parvalbumin. The lengthening of the C-terminal F helix by one residue appears to be a major feature of alpha-parvalbumins in general, owing to the homologies of the amino acid sequences. Besides the lengthening of the C-terminal helix, the classification of the leopard shark parvalbumin in the alpha-series rests upon the observation of Lys13, Leu32, Glu61 and Val66. As this is the first crystal structure description of a parvalbumin from the alpha-phylogenetic lineage, it was hoped that it would clearly determine the presence or absence of a third cation binding site in parvalbumins belonging to the alpha-lineage. In beta-pike pI 4.10 parvalbumin, Asp61 participates as a direct ligand of a third site, the satellite of the CD site. In shark parvalbumin, as in nearly all alpha-parvalbumins, one finds Glu at position 61. Unfortunately, the conformation of the polar head of Glu61 cannot be inferred from the X-ray data.(ABSTRACT TRUNCATED AT 400 WORDS)
 
  Selected figure(s)  
 
Figure 2.
Figure 2. istogram howing the umber f contacts < 3.40 ) etween water olecules and ain chain (filled ars) or side-chain open ars) atoms of the heliees and f the oops btween the helics.
Figure 9.
Figure 9. tereo diagram f ontacts between the B-helix (Tyr26, Lys27, Hisal), the BC loop 4~~36) and the C-terminal domain F-helix: la109, ln108) (p r g am PLUTO; Motherwell legg, 978). Distances (A): la109 -T1 to is31 NE2 = 3.08; Ala109 O-T1 to Lys36 C = 253; la109 -T2 to is31 E2 = 286; Gln108 OE' to yr26 OH = 2.88.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 223, 705-720) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287610 M.T.Henzl, J.J.Tanner, and A.Tan (2011).
Solution structures of chicken parvalbumin 3 in the Ca(2+)-free and Ca(2+)-bound states.
  Proteins, 79, 752-764.
PDB codes: 2kyc 2kyf
20156445 J.P.Schuermann, A.Tan, J.J.Tanner, and M.T.Henzl (2010).
Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states.
  J Mol Biol, 397, 991.
PDB codes: 2kqy 3fs7
19796207 U.Griesmeier, S.Vázquez-Cortés, M.Bublin, C.Radauer, Y.Ma, P.Briza, M.Fernández-Rivas, and H.Breiteneder (2010).
Expression levels of parvalbumins determine allergenicity of fish species.
  Allergy, 65, 191-198.  
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.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
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
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
  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
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
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.  
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.  
9733775 J.L.Banères, F.Roquet, M.Green, H.LeCalvez, and J.Parello (1998).
The cation-binding domain from the alpha subunit of integrin alpha5 beta1 is a minimal domain for fibronectin recognition.
  J Biol Chem, 273, 24744-24753.  
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.  
9738009 S.Vasudevan, T.Tsuruo, and D.R.Rose (1998).
Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
  J Biol Chem, 273, 25413-25419.
PDB code: 1bln
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
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.  
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.  
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.  
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.

 

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