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PDBsum entry 1bod

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protein links
Calcium-binding protein PDB id
1bod
Jmol
Contents
Protein chain
74 a.a. *
* Residue conservation analysis
PDB id:
1bod
Name: Calcium-binding protein
Title: The solution structures of mutant calbindin d9k's, as determ nmr, show that the calcium binding site can adopt different
Structure: Calbindin d9k. Chain: a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: intestine
NMR struc: 24 models
Authors: C.Johansson,M.Ullner,T.Drakenberg
Key ref:
C.Johansson et al. (1993). The solution structures of mutant calbindin D9k's, as determined by NMR, show that the calcium-binding site can adopt different folds. Biochemistry, 32, 8429-8438. PubMed id: 8357794 DOI: 10.1021/bi00084a007
Date:
23-Apr-93     Release date:   31-Oct-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02633  (S100G_BOVIN) -  Protein S100-G
Seq:
Struc:
79 a.a.
74 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     apical plasma membrane   2 terms 
  Biochemical function     vitamin D binding     3 terms  

 

 
DOI no: 10.1021/bi00084a007 Biochemistry 32:8429-8438 (1993)
PubMed id: 8357794  
 
 
The solution structures of mutant calbindin D9k's, as determined by NMR, show that the calcium-binding site can adopt different folds.
C.Johansson, M.Ullner, T.Drakenberg.
 
  ABSTRACT  
 
The complete 1H NMR assignments have been obtained for five mutant proteins of calbindin D9k and the three-dimensional solution structures determined for two of the mutants. The structures have been determined using distance geometry and simulated annealing, with distance constraints from NMR. All mutants have modifications in the first calcium-binding site of calbindin (the N-terminal site designated the pseudo-EF-hand). The 3D structure of the mutant with the most extensive modifications in the pseudo-EF-hand shows that the site has turned inside-out and coordinates calcium as in the normal EF-hand (the C-terminal site). In a pseudo-EF-hand loop the calcium is coordinated by main-chain carbonyls, whereas calcium in the normal EF-hand is coordinated by side-chain carboxylates. The 3D structures and 1H NMR assignments show that in order to accomplish a change in the coordinating ligands of the pseudo-EF-hand the loop must be 12 residues long and have glycine in the sixth position. It does, however, seem possible to have alanine instead of aspartic acid in the first calcium coordinating position. The overall global fold of the proteins has not been affected by the mutations in the calcium-binding site, as compared to the wild-type calbindin D9k [K├Ârdel, J., Skelton, N. J., Akke, M., & Chazin, W. J. (1993) J. Mol. Biol. (in press)]. The structures consist of two helix-calcium-binding loop-helix motifs, the so called EF-hands, and the loops are connected by a short antiparallel beta-sheet. All helices are pairwise in an antiparallel orientation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21269277 L.Santamaria-Kisiel, and G.S.Shaw (2011).
Identification of regions responsible for the open conformation of S100A10 using chimaeric S100A11-S100A10 proteins.
  Biochem J, 434, 37-48.  
15596501 D.Dell'Orco, W.F.Xue, E.Thulin, and S.Linse (2005).
Electrostatic contributions to the kinetics and thermodynamics of protein assembly.
  Biophys J, 88, 1991-2002.  
11316872 M.Håkansson, A.Svensson, J.Fast, and S.Linse (2001).
An extended hydrophobic core induces EF-hand swapping.
  Protein Sci, 10, 927-933.
PDB code: 1ht9
9485409 A.Malmendal, G.Carlstrom, C.Hambraeus, T.Drakenberg, S.Forsen, and M.Akke (1998).
Sequence and context dependence of EF-hand loop dynamics. An 15N relaxation study of a calcium-binding site mutant of calbindin D9k.
  Biochemistry, 37, 2586-2595.  
9668057 C.Franz, I.Durussel, J.A.Cox, B.W.Schäfer, and C.W.Heizmann (1998).
Binding of Ca2+ and Zn2+ to human nuclear S100A2 and mutant proteins.
  J Biol Chem, 273, 18826-18834.  
8794734 M.Sunnerhagen, G.A.Olah, J.Stenflo, S.Forsén, T.Drakenberg, and J.Trewhella (1996).
The relative orientation of Gla and EGF domains in coagulation factor X is altered by Ca2+ binding to the first EGF domain. A combined NMR-small angle X-ray scattering study.
  Biochemistry, 35, 11547-11559.
PDB codes: 1whe 1whf
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