Many calcium-binding proteins belong to the same evolutionary family and share
a type of calcium-binding domain known as the EF-hand [1,2,3,4,5]. This type of
domain consists of a twelve residue loop flanked on both side by a twelve
residue α-helical domain (see <PDB:1CLL>). In an EF-hand loop the calcium
ion is coordinated in a pentagonal bipyramidal configuration. The six residues
involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues
are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12
provides two oxygens for liganding Ca (bidentate ligand). The basic
structural/functional unit of EF-hand proteins is usually a pair of EF-hand
motifs that together form a stable four-helix bundle domain. The pairing of
EF-hand enables cooperativity in the binding of Ca2+ ions.
We list below the proteins which are known to contain EF-hand regions. For
each type of protein we have indicated between parenthesis the total number of
EF-hand regions known or supposed to exist. This number does not include
regions which clearly have lost their calcium-binding properties, or the
atypical low-affinity site (which spans thirteen residues) found in the S-100/
ICaBP family of proteins .
Aequorin and Renilla luciferin binding protein (LBP) (Ca=3).
α actinin (Ca=2).
Calcineurin B subunit (protein phosphatase 2B regulatory subunit) (Ca=4).
Calcium-binding protein from Streptomyces erythraeus (Ca=3?).
Calcium-binding protein from Schistosoma mansoni (Ca=2?).
Calcium-binding proteins TCBP-23 and TCBP-25 from Tetrahymena thermophila
Calcium-dependent protein kinases (CDPK) from plants (Ca=4).
Serine/threonine specific protein phosphatase rdgc (EC 184.108.40.206) from
Sorcin V19 from hamster (Ca=2).
Spectrin α chain (Ca=2).
Squidulin (optic lobe calcium-binding protein) from squid (Ca=4).
Troponins C; from skeletal muscle (Ca=4), from cardiac muscle (Ca=3), from
arthropods and molluscs (Ca=2).
There has been a number of attempts [7,8] to develop patterns that pick-up EF-hand regions, but these studies were made a few years ago when not so many
different families of calcium-binding proteins were known. We therefore
developed a new pattern which takes into account all published sequences. This
pattern includes the complete EF-hand loop as well as the first residue which
follows the loop and which seem to always be hydrophobic. We also developed a
profile that covers the loop and the two α helices.
Positions 1 (X), 3 (Y) and 12 (-Z) are the most conserved.
The 6th residue in an EF-hand loop is, in most cases a Gly, but the
number of exceptions to this 'rule' has gradually increased and we felt that
the pattern should include all the different residues which have been shown
to exist in this position in functional Ca-binding sites.
The pattern will, in some cases, miss one of the EF-hand regions in
some proteins with multiple EF-hand domains.
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