From Proteopedia

Revision as of 18:21, 21 September 2013

EF-hands are calcium-binding motifs found in hundreds of proteins. They bind calcium ions with high affinity (K_ds are in the micromolar range) and selectivity, and this property allows EF-hand proteins to sense changes in intracellular calcium. In unstimulated cells cellular free calcium concentrations [Ca²⁺]_c are in the nanomolar range (~10 nM in animal cells and ~200 nM in plant cells), and EF-hands are generally unoccupied by Ca²⁺. Upon stimulation, Ca²⁺ enters the cytosol from either outside the cell or from internal organelles, and [Ca²⁺]_c rises to the micromolar range. EF-hands bind Ca²⁺, and this binding causes a conformational change that alters the activity of the protein.

This page focuses on the structure of EF hands. For additional information see http://en.wikipedia.org/wiki/EF_hand.

The name EF-hand originated from the first such structure to be described, which was in the protein parvalbumin^[1]. In this protein calcium is bound by a helix-loop-helix structure that is formed by the E and F helices (letters assigned to helices in the order that they occur starting at the N-terminus). See the annotated protein sequence for carp parvalbumin here [1]. The structure resembled a hand with the forefinger pointing in the direction of the E helix, the thumb pointing in the direction of the H helix, and the remaining fingers curled to resemble the calcium-binding loop.

The loop structure is formed by the EF-hand calcium-binding motif, which contains 12 residues, and is defined in Prosite concensus pattern PS00018 ^[2]

where x indicates any residue; any residue in square brackets [] is possible at that position; none of the residues in curly brackets {} are possible: and x(2) indicates a series of two x.

The calcium ion is coordinated by seven oxygen atoms that form a pentagonal bipyramid (five atoms form the base of the pyramid and the other two the points). One oxygen is contributed by each of the side chains of residues in positions 1, 3, 5, 9; two are from the side chain of E or D at position 12; one is from the backbone of the residue at position 7; and one from water.

Below are three examples of EF-hand proteins. parvalbumin has a pair of EF-hands, calmodulin has two pair, and calcium-dependent protein kinase, has two pair in its calcium-binding domain that is attached to a protein kinase catalytic domain. As shown in these examples EF-hands often occur in pairs, which enables the cooperative binding of calcium ions. The initial scene shows the proteins in cartoon with Ca2+ in green space fill. The calcium binding domain of CDPK is blue and the kinase catalytic domain is in gold and has an ATP analog (sticks in CPK colors) bound in its active site.

Scenes numbered 1 show pairs of EF-hands in each protein, one in blue and one in gold, which are linked by the sequence shown in orchid.
Scenes numbered 2 isolate one E-F hand: the eponymous E-F hand of parvalbumen, E-F hand I (they are numbered I-IV) in calmodulin, and E-F hand IV of CDPK.
Scenes numbered 3 show the calcium binding loops, which are shown in the same orientation. The five residues that contribute oxygens form the base of pyramid are distributed around the equator of the calcium ion, the "north" pyramid point is the oxygen from water, and the "south" point is the invariant D at position 1 in the motif.

References

1. ↑ Kretsinger RH, Nockolds CE. Carp muscle calcium-binding protein. II. Structure determination and general description. J Biol Chem. 1973 May 10;248(9):3313-26. PMID:4700463
2. ↑ http://prosite.expasy.org/PDOC00018