PDBsum entry 1b8r

Go to PDB code: 
protein metals links
Calcium binding protein PDB id
Protein chain
108 a.a. *
_CA ×2
Waters ×89
* Residue conservation analysis
PDB id:
Name: Calcium binding protein
Title: Parvalbumin
Structure: Protein (parvalbumin). Chain: a. Engineered: yes. Mutation: yes
Source: Cyprinus carpio. Common carp. Organism_taxid: 7962. Expressed in: escherichia coli. Expression_system_taxid: 562
1.90Å     R-factor:   0.177     R-free:   0.270
Authors: M.S.Cates,M.B.Berry,E.L.Ho,Q.Li,J.D.Potter,G.N.Phillips Jr.
Key ref:
M.S.Cates et al. (1999). Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin. Structure Fold Des, 7, 1269-1278. PubMed id: 10545326 DOI: 10.1016/S0969-2126(00)80060-X
02-Feb-99     Release date:   09-Feb-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02618  (PRVB_CYPCA) -  Parvalbumin beta
108 a.a.
108 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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


DOI no: 10.1016/S0969-2126(00)80060-X Structure Fold Des 7:1269-1278 (1999)
PubMed id: 10545326  
Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin.
M.S.Cates, M.B.Berry, E.L.Ho, Q.Li, J.D.Potter, G.N.Phillips.
BACKGROUND: The EF-hand family is a large set of Ca(2+)-binding proteins that contain characteristic helix-loop-helix binding motifs that are highly conserved in sequence. Members of this family include parvalbumin and many prominent regulatory proteins such as calmodulin and troponin C. EF-hand proteins are involved in a variety of physiological processes including cell-cycle regulation, second messenger production, muscle contraction, microtubule organization and vision. RESULTS: We have determined the structures of parvalbumin mutants designed to explore the role of the last coordinating residue of the Ca(2+)-binding loop. An E101D substitution has been made in the parvalbumin EF site. The substitution decreases the Ca(2+)-binding affinity 100-fold and increases the Mg(2+)-binding affinity 10-fold. Both the Ca(2+)- and Mg(2+)-bound structures have been determined, and a structural basis has been proposed for the metal-ion-binding properties. CONCLUSIONS: The E101D mutation does not affect the Mg(2+) coordination geometry of the binding loop, but it does pull the F helix 1.1 A towards the loop. The E101D-Ca(2+) structure reveals that this mutant cannot obtain the sevenfold coordination preferred by Ca(2+), presumably because of strain limits imposed by tertiary structure. Analysis of these results relative to previously reported structural information supports a model wherein the characteristics of the last coordinating residue and the plasticity of the Ca(2+)-binding loop delimit the allowable geometries for the coordinating sphere.
  Selected figure(s)  
Figure 3.
Figure 3. Delta distance plots of parvalbumin mutants versus wild type. (a) F102W-Ca^2+ minus wild-type carp-Ca^2+. Contours for D of 1 or greater. The absolute values of the differences in the inter-residue distances between the F102W mutant and wild type are all < 1 , except at the termini. The N terminus appears to be especially dynamic. (b) PVEF-Ca^2+ minus wild-type carp-Ca^2+. Contours for D of 1 or greater. The mutation at residue 51 in PVEF affects interresidue distances primarily in the CD loop (residues 51-62). There also appears to be some variation from wild-type in the C helix (residues 40-50).
  The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 1269-1278) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21312310 W.Ohashi, H.Hirota, and T.Yamazaki (2011).
Solution structure and fluctuation of the Mg(2+)-bound form of calmodulin C-terminal domain.
  Protein Sci, 20, 690-701.
PDB code: 2rrt
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.  
19998355 Y.Zhang, H.Tan, G.Chen, and Z.Jia (2010).
Investigating the disorder-order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation.
  J Mol Recognit, 23, 360-368.  
19604472 D.S.Glazer, R.J.Radmer, and R.B.Altman (2009).
Improving structure-based function prediction using molecular dynamics.
  Structure, 17, 919-929.  
19622856 F.Hoh, A.Cavé, M.P.Strub, J.L.Banères, and A.Padilla (2009).
Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure.
  Acta Crystallogr D Biol Crystallogr, 65, 733-743.
PDB code: 3f45
19274659 S.H.Arif (2009).
A Ca(2+)-binding protein with numerous roles and uses: parvalbumin in molecular biology and physiology.
  Bioessays, 31, 410-421.  
20003365 T.Liu, and R.B.Altman (2009).
Prediction of calcium-binding sites by combining loop-modeling with machine learning.
  BMC Struct Biol, 9, 72.  
  18229697 D.S.Glazer, R.J.Radmer, and R.B.Altman (2008).
Combining molecular dynamics and machine learning to improve protein function recognition.
  Pac Symp Biocomput, (), 332-343.  
18989041 P.Yao, A.Dhanik, N.Marz, R.Propper, C.Kou, G.Liu, H.van den Bedem, J.C.Latombe, I.Halperin-Landsberg, and R.B.Altman (2008).
Efficient algorithms to explore conformation spaces of flexible protein loops.
  IEEE/ACM Trans Comput Biol Bioinform, 5, 534-545.  
17081122 T.Guevara, N.Mallorquí-Fernández, R.García-Castellanos, S.García-Piqué, G.Ebert Petersen, C.Lauritzen, J.Pedersen, J.Arnau, F.X.Gomis-Rüth, and M.Solà (2006).
Papaya glutamine cyclotransferase shows a singular five-fold beta-propeller architecture that suggests a novel reaction mechanism.
  Biol Chem, 387, 1479-1486.
PDB code: 2iwa
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.  
11114499 A.Lewit-Bentley, and S.Réty (2000).
EF-hand calcium-binding proteins.
  Curr Opin Struct Biol, 10, 637-643.  
  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.  
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.