PDBsum entry 2f33

Metal binding protein

PDB id: 2f33

Contents

Protein chain

261 a.a. *

* Residue conservation analysis

PDB id:

2f33

Name:

Metal binding protein

Title:

Nmr solution structure of ca2+-loaded calbindin d28k

Structure:

Calbindin. Chain: a. Synonym: vitamin d-dependent calcium-binding protein, avian-type, calbindin d28, d-28k, spot 35 protein. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: calb1. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

10 models

Authors:

D.J.Kojetin,R.A.Venters,D.R.Kordys,R.J.Thompson,R.Kumar,J.Cavanagh

Key ref:

D.J.Kojetin et al. (2006). Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D(28K). Nat Struct Mol Biol, 13, 641-647. PubMed id: 16799559 DOI: 10.1038/nsmb1112

Date:

18-Nov-05 Release date: 04-Jul-06

Protein chain

P07171  (CALB1_RAT) -  Calbindin from Rattus norvegicus

Seq: 261 a.a.

Struc: 261 a.a.

DOI no: 10.1038/nsmb1112

Nat Struct Mol Biol 13:641-647 (2006)

PubMed id: 16799559

Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D(28K).

D.J.Kojetin, R.A.Venters, D.R.Kordys, R.J.Thompson, R.Kumar, J.Cavanagh.

ABSTRACT

Calbindin-D(28K) is a Ca2+-binding protein, performing roles as both a calcium buffer and calcium sensor. The NMR solution structure of Ca2+-loaded calbindin-D(28K) reveals a single, globular fold consisting of six distinct EF-hand subdomains, which coordinate Ca2+ in loops on EF1, EF3, EF4 and EF5. Target peptides from Ran-binding protein M and myo-inositol monophosphatase, along with a new target from procaspase-3, are shown to interact with the protein on a surface comprised of alpha5 (EF3), alpha8 (EF4) and the EF2-EF3 and EF4-EF5 loops. Fluorescence experiments reveal that calbindin-D(28K) adopts discrete hydrophobic states as it binds Ca2+. The structure, binding interface and hydrophobic characteristics of Ca2+-loaded calbindin-D(28K) provide the first detailed insights into how this essential protein may function. This structure is one of the largest high-resolution NMR structures and the largest monomeric EF-hand protein to be solved to date.

Selected figure(s)

Figure 2.
Figure 2. Long-distance EF-hand pair-pair interactions. C superimposition of the ten lowest-energy structures of Ca^2+-loaded calbindin-D[28K], showing representative pair-pair interactions between EF1-EF2 and EF3-EF4 (a,b), and EF3-EF4 and EF5-EF6 (c,d). There is a 180° rotation about the vertical axis between a and b and between c and d.

Figure 3.
Figure 3. Peptide titrations of Ca^2+-loaded calbindin-D[28K] and binding interface. (a–c) Selected regions of the 2D ^1H[N]-^15N TROSY spectra of calbindin-D[28K] binding to target peptides from (a) RanBPM (LASIKNR), (b) IMPase (ISSIKEKYPSHS) and (c) the pro-domain of procaspase-3 (SKSIKNLEP). The spectra were collected at peptide/protein ratios of 0:1 (black), 1:1 (green), 2:1 (dark blue), 4:1 (light blue), 8:1 (red) and 16:1 (pink). Residues showing chemical shift changes or line broadening are affected by peptide binding. (d) RanBPM peptide binding characteristics mapped onto the structure ensemble of Ca^2+-loaded calbindin-D[28K], displayed as a PyMOL surface plot. Residues are highlighted according to trends observed as results of the peptide titration: red, peak linewidth broadening and disappearance; yellow, substantial change in chemical shift; blue, moderate linewidth broadening and change in chemical shift; gray, residues unobservable at 25 °C owing to conformational exchange on an intermediate NMR timescale. Peptides derived from IMPase and procaspase-3 show similar binding traits (see text).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 641-647) copyright 2006.

Figures were selected by an automated process.