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PDBsum entry 1bu3

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protein metals links
Calcium binding PDB id
1bu3
Jmol
Contents
Protein chain
109 a.a. *
Metals
_CA ×2
Waters ×114
* Residue conservation analysis
PDB id:
1bu3
Name: Calcium binding
Title: Refined crystal structure of calcium-bound silver hake (pi 4.2) parvalbumin at 1.65 a.
Structure: Calcium-binding protein. Chain: a. Fragment: calcium-binding domain
Source: Merluccius bilinearis. Silver hake. Organism_taxid: 79698. Tissue: muscle
Resolution:
1.65Å     R-factor:   0.214     R-free:   0.251
Authors: R.C.Richardson,D.J.Nelson,W.E.Royer,D.J.Harrington
Key ref:
S.P.Revett et al. (1997). Characterization of a helix-loop-helix (EF hand) motif of silver hake parvalbumin isoform B. Protein Sci, 6, 2397-2408. PubMed id: 9385642 DOI: 10.1002/pro.5560061113
Date:
30-Aug-98     Release date:   10-Aug-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56503  (PRVB_MERBI) -  Parvalbumin beta
Seq:
Struc:
108 a.a.
108 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: 10.1002/pro.5560061113 Protein Sci 6:2397-2408 (1997)
PubMed id: 9385642  
 
 
Characterization of a helix-loop-helix (EF hand) motif of silver hake parvalbumin isoform B.
S.P.Revett, G.King, J.Shabanowitz, D.F.Hunt, K.L.Hartman, T.M.Laue, D.J.Nelson.
 
  ABSTRACT  
 
Parvalbumins are a class of calcium-binding proteins characterized by the presence of several helix-loop-helix (EF-hand) motifs. It is suspected that these proteins evolved via intragene duplication from a single EF-hand. Silver hake parvalbumin (SHPV) consists of three EF-type helix-loop-helix regions, two of which have the ability to bind calcium. The three helix-loop-helix motifs are designated AB, CD, and EF, respectively. In this study, native silver hake parvalbumin isoform B (SHPV-B) has been sequenced by mass spectrometry. The sequence indicates that this parvalbumin is a beta-lineage parvalbumin. SHPV-B was cleaved into two major fragments, consisting of the ABCD and EF regions of the native protein. The 33-amino acid EF fragment (residues 76-108), containing one of the calcium ion binding sites in native SHPV-B, has been isolated and studied for its structural characteristics, ability to bind divalent and trivalent cations, and for its propensity to undergo metal ion-induced self-association. The presence of Ca2+ does not induce significant secondary structure in the EF fragment. However, NMR and CD results indicate significant secondary structure promotion in the EF fragment in the presence of the higher charge-density trivalent cations. Sedimentation equilibrium analysis results show that the EF fragment exists in a monomer-dimer equilibrium when complexed with La3+.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Proteolytic map of SHPV-B showing fragments generated for sequencing by mass spectrometry. Ile andLeu are shown as X because these residues cannot e distinguished from one another due to their identical residue weight.
Figure 10.
Fig. 10. Upfieldregion f 1D `H NMR spectra (at 500 MHz) of (A) 0.07 mMEF ragment in -98 D20 withtwofoldmolarexcess of La'', pH 6.1,and (B) 0.07 mM Ffragment n -98%D20 ith twofoldmolar excess of Ca2+, pH6.4.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (1997, 6, 2397-2408) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16927426 M.Carrera, B.Cañas, C.Piñeiro, J.Vázquez, and J.M.Gallardo (2006).
Identification of commercial hake and grenadier species by proteomic analysis of the parvalbumin fraction.
  Proteomics, 6, 5278-5287.  
11948786 K.Julenius, J.Robblee, E.Thulin, B.E.Finn, R.Fairman, and S.Linse (2002).
Coupling of ligand binding and dimerization of helix-loop-helix peptides: spectroscopic and sedimentation analyses of calbindin D9k EF-hands.
  Proteins, 47, 323-333.  
  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.  
9778361 J.G.Stout, Q.Zhou, T.Wiedmer, and P.J.Sims (1998).
Change in conformation of plasma membrane phospholipid scramblase induced by occupancy of its Ca2+ binding site.
  Biochemistry, 37, 14860-14866.  
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.