EF hand
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| Calmodulin with four EF-Hand-motifs. | ||
| EF hand | ||
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| Identifiers | ||
| Symbol | efhand | |
| Pfam | PF00036 | |
| InterPro | IPR002048 | |
| PROSITE | PDOC00018 | |
| SCOP | 1osa | |
| OPM protein | 1djx | |
| Available PDB structures:
1s6jA:375-402 1s6iA:375-403 1m39A:141-169 2a4jA:141-169 1oqpA:138-166 2bbnA:121-148 2bkhB:121-148 1mxeA:121-148 4cln :121-148 2bbmA:121-148 1cdmA:121-146 1lin :121-148 2bkiB:121-148 1oojA:121-148 1osa :121-148 1clm :121-147 1n0yB:121-148 1exrA:121-148 1rfjA:121-149 1ggzA:121-148 1ak8 :48-75 1sw8A:48-76 1j7oA:48-76 1f70A:48-76 1r2uA:56-84 1r6pA:56-84 1j1eA:56-84 |
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The EF hand is a helix-turn-helix structural domain found in a large family of calcium-binding proteins. It consists of two alpha helices positioned roughly perpendicular to one another and linked by a short loop region (usually about 12 amino acids) that usually binds calcium ions. The motif takes its name from traditional nomenclature used in describing the protein parvalbumin, which contains three such motifs and is probably involved in muscle relaxation via its calcium-binding activity. EF hands also appear in each structural domain of the signaling protein calmodulin and in the muscle protein troponin-C.
Contents |
[edit] Binding site
The calcium ion is bound by both protein backbone atoms and by amino acid side chains, specifically those of the acidic amino acid residues, aspartate and glutamate. These residues are negatively charged and will make a charge-interaction with the positively charged calcium ion. The EF hand motif was among the first structural motifs whose sequence requirements were analyzed in detail. Five of the loop residues bind calcium and thus have a strong preference for oxygen-containing side chains, especially aspartate and glutamate. The sixth residue in the loop is necessarily glycine due to the conformational requirements of the backbone. The remaining residues are typically hydrophobic and form a hydrophobic core that binds the stabilizes the two helices.
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).
[edit] Classification
The EF-hands can be divided into two classes: signaling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.
[edit] Subfamilies
[edit] Human proteins containing this domain
ACTN1; ACTN2; ACTN3; ACTN4; APBA2BP; AYTL1; AYTL2; C14orf143; CABP1; CABP2; CABP3; CABP4; CABP5; CABP7; CALB1; CALB2; CALM2; CALM3; CALML3; CALML4; CALML5; CALML6; CALN1; CALU; CAPN1; CAPN11; CAPN2; CAPN3; CAPN9; CAPNS1; CAPNS2; CAPS; CAPS2; CAPSL; CBARA1; CETN1; CETN2; CETN3; CHP; CHP2; CIB1; CIB2; CIB3; CIB4; CRNN; DGKA; DGKB; DGKG; DST; DUOX1; DUOX2; EFCAB1; EFCAB2; EFCAB4A; EFCAB4B; EFCAB6; EFCBP1; EFCBP2; EFHA1; EFHA2; EFHB; EFHC1; EFHD1; EFHD2; EPS15; EPS15L1; FKBP10; FKBP14; FKBP7; FKBP9; FKBP9L; FREQ; FSTL1; FSTL5; GCA; GPD2; GUCA1A; GUCA1B; GUCA1C; hippocalcin; HPCAL1; HPCAL4; HZGJ; IFPS; ITSN1; ITSN2; KCNIP1; KCNIP2; KCNIP3; KCNIP4; KIAA1799; LCP1; MACF1; MRLC2; MRLC3; MST133; MYL1; MYL2; MYL5; MYL6B; MYL7; MYL9; MYLC2PL; MYLPF; NCALD; NIN; NKD1; NKD2; NLP; NOX5; NUCB1; NUCB2; OCM; PDCD6; PEF1; PKD2; PLCD1; PLCD4; PLCH1; PLCH2; PLS1; PLS3; PP1187; PPEF1; PPEF2; PPP3R1; PPP3R2; PRKCSH; PVALB; RAB11FIP3; RASEF; RASGRP; RASGRP1; RASGRP2; RASGRP3; RCN1; RCN2; RCN3; RCV1; RCVRN; REPS1; RHBDL3; RHOT1; RHOT2; RPTN; RYR2; RYR3; S100A1; S100A11; S100A12; S100A6; S100A8; S100A9; S100B; S100G; S100Z; SCAMC-2; SCGN; SDF4; SLC25A12; SLC25A13; SLC25A23; SLC25A24; SLC25A25; SPATA21; SPTA1; SPTAN1; SRI; TBC1D9; TBC1D9B; TCHH; TESC; TNNC1; TNNC2; USP32; VSNL1; ZZEF1;
[edit] See also
Another distinct calcium-binding motif composed of alpha helices is the dockerin domain.
[edit] External links
[edit] Further reading
- Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY.
- Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories. Nakayama S, Moncrief ND, Kretsinger RH; J Mol Evol 1992;34:416-448. PubMed
- Comparison of terbium (III) luminescence enhancement in mutants of EF hand calcium binding proteins. Hogue CW, MacManus JP, Banville D, Szabo AG; J Biol Chem 1992;267:13340-13347. PubMed
- EF-hand motifs in inositol phospholipid-specific phospholipase C. Bairoch A, Cox JA; FEBS Lett 1990;269:454-456.PubMed
- The evolving model of calmodulin structure, function and activation. Finn BE, Forsen S; Structure 1995;3:7-11. PubMed
| Protein secondary structure | ||
|---|---|---|
| Helices: | α-helix | 310 helix | π-helix | β-helix | Polyproline helix | Collagen helix | |
| Extended: | β-strand | Turn | Beta hairpin | Beta bulge | α-strand | |
| Supersecondary: | Coiled coil | Helix-turn-helix | EF hand | |
| Secondary structure propensities of amino acids | ||
| Helix-favoring: | Methionine | Alanine | Leucine | Glutamic acid | Glutamine | Lysine | |
| Extended-favoring: | Threonine | Isoleucine | Valine | Phenylalanine | Tyrosine | Tryptophan | |
| Disorder-favoring: | Glycine | Serine | Proline | Asparagine | Aspartic acid | |
| No preference: | Cysteine | Histidine | Arginine | |
| ←Primary structure | Tertiary structure→ | |
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