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Structural Basis for Diversity of the EF-Hand Calcium-Binding Proteins

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Structural Basis for Diversity of the EF-Hand Calcium-Binding Proteins doi:10.1016/j.jmb.2006.03.066 J. Mol. Biol. (2006) 359, 509–525 REVIEW Structural Basis for Diversity of the EF-hand Calcium-binding Proteins Zenon Grabarek Boston Biomedical Research The calcium binding proteins of the EF-hand super-family are involved in Institute, Watertown, MA the regulation of all aspects of cell function. These proteins exhibit a great C 02472, USA diversity of composition, structure, Ca2 -binding and target interaction C properties. Here, our current understanding of the Ca2 -binding mechanism is assessed. The structures of the EF-hand motifs containing C 11–14 amino acid residues in the Ca2 -binding loop are analyzed C within the framework of the recently proposed two-step Ca2 -binding mechanism. A hypothesis is put forward that in all EF-hand proteins the C Ca2 -binding and the resultant conformational responses are governed C by the central structure connecting the Ca2 -binding loops in the two-EF- hand domain. This structure, named EFb-scaffold, defines the position C of the bound Ca2 , and coordinates the function of the N-terminal (variable and flexible) with the C-terminal (invariable and rigid) parts of C the Ca2 -binding loop. It is proposed that the nature of the first ligand of C the Ca2 -binding loop is an important determinant of the conformational change. Additional factors, including the interhelical contacts, the length, structure and flexibility of the linker connecting the EF-hand motifs, and C the overall energy balance provide the fine-tuning of the Ca2 -induced conformational change in the EF-hand proteins. q 2006 Elsevier Ltd. All rights reserved. Keywords: EF-hand; calcium binding proteins; structure and function; calcium signaling C Introduction are triggered by the simple event of the Ca2 attracting six to seven oxygen atoms of the EF-hand. The term “EF-hand” was coined by R. H. The EF-hand proteins’ role is to “translate” that C Kretsinger over 30 years ago for the Ca2 -binding simple regulatory signal into various functional variant of a helix-loop-helix motif discovered in the responses. The exceptional versatility of the EF- C structure of parvalbumin, a small Ca2 -binding hand motif is clearly reflected in the growing protein isolated from carp muscle.1 The EF-hand database of three-dimensional structures of EF- motifs were then identified in the amino acid hand proteins revealing a great diversity of sequence of troponin C,2 the myosin light chains,3 conformations, domain organization, and structural the ubiquitous calmodulin,4,5 and in many other responses to calcium.12,13 However, our under- C Ca2 -binding proteins.6,7 Today, there are more standing of the structural principles that underlie than 3000 EF-hand related entries in the NCBI this versatility and govern the function of EF-hand Reference Sequences Data Bank. Calcium and the proteins is far from adequate. The problem is C EF-hand Ca2 -binding proteins have been recog- that there are still very few proteins for which the nized as the key players in all aspects of cell high-resolution X-ray crystallographic structures of C function, starting with a cell’s birth during mitosis both the apo and the Ca2 -bound forms are and ending with its apoptotic death.8–11 At the most available. In recent years remarkable progress has fundamental level, these diverse cellular functions been made owing to the development and use of NMR techniques, which provide invaluable infor- mation on the dynamical properties of the EF-hand Abbreviations used: CaM, calmodulin; TnC, troponin proteins and enable study of transient confor- 14–18 C; PDB, Protein Data Bank. mational states. Unfortunately, NMR tech- E-mail address of the author [email protected] niques do not provide sufficiently precise 0022-2836/$ - see front matter q 2006 Elsevier Ltd. All rights reserved. 510 Review: Diversity of Calcium-binding Proteins information on the calcium-binding loops,19 which residue of the paired EF-hand, a part of the short C are of particular interest since the calcium ligands b-sheet connecting the two Ca2 -binding loops 21. C are critical for transmitting the conformational The composition and the length of the Ca2 - C changes associated with the Ca2 -binding event binding loops vary significantly among the to the rest of the protein. EF-hand proteins. The N-terminal EF-hand in There are several excellent reviews on the calbindin D9k, the vitamin D-dependent calcium structure and function of calcium-binding proteins. binding protein from intestine, has a 14-residue C An extensive analysis of the Ca2 -binding sites in loop and except for the C-terminal glutamate, all proteins can be found in the article by McPhalen protein ligands are the main-chain carbonyl oxygen et al.20 The EF-hand proteins specifically are atoms.38,39 Despite such radical departure from discussed by Strynadka & James.21 The diversity the “normal” mode of binding, the pentagonal C C in the organization, packing and response to Ca2 bipyramid Ca2 -ligand geometry and the high C in EF-hand proteins was reviewed by Nelson & affinity for Ca2 are preserved. This variant of the Chazin.12 and most recently by Ikura & Ames.22 EF-hand motif referred to as the pseudo EF-hand is Evenas et al.23 published an overview of the found in members of the S100 protein family. More C intra- and extra-cellular Ca2 -signaling from the recently, structures of EF-hand proteins containing C structural perspective. There are several reviews an 11-residue Ca2 -binding loop (calpain,40,41 C focused on the Ca2 -binding properties of the grancalcin,42 ALG-243)ora13-residueloop EF-hand proteins,24–28 and on the target binding (SPARC/osteonectin/BM-4044) became available mechanisms.29–35 A selection of articles covering and provided evidence that similar pentagonal C C broad aspects of Ca2 -signaling can be found in the bipyramid geometry of Ca2 -coordination can be book edited by Ernesto Carafoli & Claude Klee.36 achieved in several different ways. In Table 1 there Finally, specific information on each of the many are examples of amino acid sequences of various subfamilies of EF-hand proteins can be found in EF-hand motifs. It is striking that all the insertions dedicated reviews, too numerous to list here. and deletions are localized in the N-terminal part of The present work is focused on the mechanism by the loop, whereas the C-terminal part is constant in C which Ca2 drives the conformational change in length. Differences in the loop length and compo- EF-hand proteins. Selected high-resolution X-ray sition lead to different backbone folding, and often crystallographic structures of EF-hand proteins the main-chain carbonyl oxygen atoms are involved C C representative of diverse families are analyzed in Ca2 -binding. It appears that the Ca2 -binding within the framework of the recently proposed ligand is defined by the backbone conformation. For C two-step Ca2 -binding mechanism37 and example in calcyclin (the S100A6 protein) Glu23 C compared in a conformation-independent frame (Y position) and Asp25 (Z position) bind Ca2 with of reference. A hypothesis is put forward that their main-chain carbonyl rather than the side-chain C Ca2 -binding and the resultant conformational carboxyl groups. Yet, some structural flexibility is response in all two-EF-hand domains is governed possible. Cates et al.45 found that a substitution of C by the central structure named EFb-scaffold. Some Ala for Asp in the first position of the Ca2 -binding structural features of the EF-hand motif that shape loop II of parvalbumin causes the incoming helix to the conformational change are discussed. shift slightly to enable the main-chain carbonyl oxygen to substitute for the missing carboxyl. The variability of the N-terminal part of the C Structure of the EF-hand Ca2 -binding loop is, in fact, much greater than the examples in Table 1 might suggest. The EF-hand The most common (canonical) EF-hand has a 12- I of CIB1, a protein related to the neuronal calcium C residue Ca2 -binding loop that starts with an sensors (NCS) has a 20-residue loop46 (PDB code C C aspartate and ends with a glutamate. The Ca2 – 1XO5) and KChIP1, the Kv4 K channel interacting C ligand geometry in small molecule-Ca2 complexes protein has an EF-hand with a ten-residue loop47 C is octahedral, which when applied to the Ca2 –EF- (PDB code 1S1E). Neither loop is capable of C hand complex provides a convenient assignment of Ca2 -binding, but the respective domains preserve the ligands in the orthogonal coordinate system the general EF-hand topology including the short C centered on the Ca2 , and the X,Y,Z axes defined by b-sheet hydrogen bonding with the pair-mate C the first three Ca2 ligands of the loop. However, in EF-hand. C most EF-hand proteins Ca2 is linked to seven The glutamate residue in the last coordinating oxygen atoms arranged in a pentagonal bipyramid. position and its fixed spacing from the KY ligand The Glu residue in the last position of the loop (KZ appear to be required for the pentagonal bipyramid ligand) contributes two oxygen atoms of its coordination geometry. Departure from this rule C g-carboxyl group (a bidentate ligand). In all leads to a different Ca2 -ligand geometry. One known structures of EF-hand proteins the central example is the substitution of Asp for Glu in the KZ C residue of the Ca2 -binding loop (the KY position) position of EF-hand I in the regulatory light chain of C binds Ca2 with the main-chain carbonyl oxygen myosin (Table 1), which leads to preference for C C atom.
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