PDBsum entry 1cdn

Calcium-binding protein

PDB id: 1cdn

Contents

Protein chain

75 a.a. *

* Residue conservation analysis

PDB id:

1cdn

Name:

Calcium-binding protein

Title:

Solution structure of (cd2+)1-calbindin d9k reveals details of the stepwise structural changes along the apo--> (ca2+)ii1--> (ca2+)i,ii2 binding pathway

Structure:

Calbindin d9k. Chain: a. Synonym: intestinal calcium-binding protein, icbp, icabp, cabp9k, s100d. Engineered: yes. Mutation: yes. Other_details: bovine minor a form, cadmium-half-saturated, cadmium ion is bound in c-terminal site

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Gene: icabp. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

24 models

Authors:

M.Akke,S.Forsen,W.J.Chazin

Key ref:

M.Akke et al. (1995). Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo-->(Ca2+)II1-->(Ca2+)I,II2 binding pathway. J Mol Biol, 252, 102-121. PubMed id: 7666423 DOI: 10.1006/jmbi.1995.0478

Date:

04-Aug-95 Release date: 14-Nov-95

Protein chain

P02633  (S100G_BOVIN) -  Protein S100-G from Bos taurus

Seq: 79 a.a.

Struc: 75 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1995.0478

J Mol Biol 252:102-121 (1995)

PubMed id: 7666423

Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo-->(Ca2+)II1-->(Ca2+)I,II2 binding pathway.

M.Akke, S.Forsén, W.J.Chazin.

ABSTRACT

The three-dimensional solution structure of (Cd2+)1-calbindin D9k has been determined by distance geometry, restrained molecular dynamics and relaxation matrix calculations using experimental constraints obtained from two-dimensional 1H and 15N-1H NMR spectroscopy. The final input data consisted of 1055 NOE distance constraints and 71 dihedral angle constraints, corresponding to 15 constraints per residue on average. The resulting ensemble of 24 structures has no distance or dihedral angle constraints consistently violated by more than 0.07 A and 1.8 degrees, respectively. The structure is characteristic of an EF-hand protein, with two helix-loop-helix calcium binding motifs joined by a flexible linker, and a short anti-parallel beta-type interaction between the two ion-binding sites. The four helices are well defined with a root mean square deviation from the mean coordinates of 0.35 A for the backbone atoms. The structure of the half-saturated cadmium state was compared with the previously determined solution structures of the apo and fully calcium saturated calbindin D9k. The comparisons were aided by introducing the ensemble averaged distance difference matrix as a tool for analyzing differences between two ensembles of structures. Detailed analyses of differences between the three states in backbone and side-chain dihedral angles, hydrogen bonds, interatomic distances, and packing of the hydrophobic core reveal the reorganization of the protein that occurs upon ion binding. Overall, it was found that (Cd2+)1-calbindin D9k, representing the half-saturated calcium state with an ion in site II, is structurally more similar to the fully calcium-saturated state than the apo state. Thus, for the binding sequence apo-->(Ca2+)II1-->(Ca2+)I,II2, the structural changes occurring upon ion binding are most pronounced for the first binding step, an observation that bears significantly on the molecular basis for cooperative calcium binding in calbindin D9k.

Selected figure(s)

Figure 7.
Figure 7. The distance difference matrix visualized on the structure. The average backbone coordinates of the apo (A, B) and (Cd 2+ )1 (C, D) ensembles with lines connecting pairs of atoms, corresponding to the DDMs shown in Figures 6A and B, respectively. A and C show side views with the molecules oriented as in Figure 2, while B and D show top views looking down towards the ion binding lops, with the Cd 2+ -filled site above the empty N-terminal site. The colorcoding is the same as in Figure 6. For clarity, only significant distance differences with an absolute value larger than 2.0 Å are included, and elements of the DDM involving residues K1-P3 have been omitted. Prepared using GRASP (Nicholls et al., 1991).

Figure 9.
Figure 9. Comparison of the solution structures of the apo (blue), (Cd 2+ )1 (green) and (Ca 2+ )2 (red) states. A, Helix I (P3--A15) and the side-chains of L6, I9, F10, Y13, A14 and A15. B, helix II (K25--F36) and the side-chains of L28, L31, L32 and F36. C, Helix III (T45--D54) and the side-chains of F50 and L53. D, Helix IV (F63--I73) and the side-chains of F63, F66, V68, V70 and I73 together with F36. The structures have been oriented to facilitate viewing of specific structural similarities/differences and only well-defined side-chains are shown. The Figures were prepared as for Figure 8.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 252, 102-121) copyright 1995.

Figures were selected by an automated process.