The three-dimensional structure of Ca2+-bound calcyclin: implications for Ca2+-signal transduction by S100 proteins

Sastry, Mallika; Ketchem, Randal R.; Crescenzi, Orlando; Weber, Christoph K.; Lubienski, Michael J.; Hidaka, Hiroyoshi; Chazin, Walter J.

doi:10.1016/s0969-2126(98)00023-9

Cited by 123 publications

(97 citation statements)

References 41 publications

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“…Ca 2þ bound, closed EF-hand has only been reported for two other EF-hand calcium sensors [calpain 40 and cardiac troponin C (cTnC) 41 ] and in the pseudo-EF-hand of S100 proteins (calcyclin 42 and S100B 43 ).…”

Section: Discussionmentioning

confidence: 99%

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Park

Ames

2011

Protein Science

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Calcium-binding protein 1 (CaBP1), a neuron-specific member of the calmodulin (CaM) superfamily, regulates the Ca 21 -dependent activity of inositol 1,4,5-triphosphate receptors (InsP3Rs) and various voltage-gated Ca 21 channels. Here, we present the NMR structure of fulllength CaBP1 with Ca 21 bound at the first, third, and fourth EF-hands. A total of 1250 nuclear Overhauser effect distance measurements and 70 residual dipolar coupling restraints define the overall main chain structure with a root-mean-squared deviation of 0.54 Å (N-domain) and 0.48 Å (C-domain). The first 18 residues from the N-terminus in CaBP1 (located upstream of the first EFhand) are structurally disordered and solvent exposed. The Ca 21 -saturated CaBP1 structure contains two independent domains separated by a flexible central linker similar to that in calmodulin and troponin C. The N-domain structure of CaBP1 contains two EF-hands (EF1 and EF2), both in a closed conformation [interhelical angles 5 129°(EF1) and 142°(EF2)]. The C-domain contains EF3 and EF4 in the familiar Ca 21 -bound open conformation [interhelical angles 5 105°( EF3) and 91°(EF4)]. Surprisingly, the N-domain adopts the same closed conformation in the presence or absence of Ca 21 bound at EF1. The Ca 21 -bound closed conformation of EF1 is reminiscent of Ca 21 -bound EF-hands in a closed conformation found in cardiac troponin C and calpain. We propose that the Ca 21 -bound closed conformation of EF1 in CaBP1 might undergo an induced-fit opening only in the presence of a specific target protein, and thus may help explain the highly specialized target binding by CaBP1.

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Section: Discussionmentioning

confidence: 99%

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Park

Ames

2011

Protein Science

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“…The basic organization of the S100 proteins is a symmetric, antiparallel homodimer, in which the N-and C-terminal helices (helices 1 and 4) from each subunit interact to form a stable four helix bundle that serves as the dimer interface. Calcium binding to the C-terminal typical EF-hand significantly alters the angle between helices 3 and 4, which flank the C-terminal Ca 2þ -binding loop, and exposes a hydrophobic cleft that constitutes a binding surface for target proteins (3)(4)(5). Thus the S100 proteins operate as calcium-activated switches that bind and regulate the activity of diverse protein targets.…”

mentioning

confidence: 99%

Phenothiazines inhibit S100A4 function by inducing protein oligomerization

Malashkevich

Dulyaninova

Ramagopal

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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S100A4, a member of the S100 family of Ca 2þ -binding proteins, regulates carcinoma cell motility via interactions with myosin-IIA. Numerous studies indicate that S100A4 is not simply a marker for metastatic disease, but rather has a direct role in metastatic progression. These observations suggest that S100A4 is an excellent target for therapeutic intervention. Using a unique biosensorbased assay, trifluoperazine (TFP) was identified as an inhibitor that disrupts the S100A4/myosin-IIA interaction. To examine the interaction of S100A4 with TFP, we determined the 2.3 Å crystal structure of human Ca 2þ -S100A4 bound to TFP. Two TFP molecules bind within the hydrophobic target binding pocket of Ca 2þ -S100A4 with no significant conformational changes observed in the protein upon complex formation. NMR chemical shift perturbations are consistent with the crystal structure and demonstrate that TFP binds to the target binding cleft of S100A4 in solution. Remarkably, TFP binding results in the assembly of five Ca 2þ -S100A4/TFP dimers into a tightly packed pentameric ring. Within each pentamer most of the contacts between S100A4 dimers occurs through the TFP moieties. The Ca 2þ -S100A4/prochlorperazine (PCP) complex exhibits a similar pentameric assembly. Equilibrium sedimentation and cross-linking studies demonstrate the cooperative formation of a similarly sized S100A4/TFP oligomer in solution. Assays examining the ability of TFP to block S100A4-mediated disassembly of myosin-IIA filaments demonstrate that significant inhibition of S100A4 function occurs only at TFP concentrations that promote S100A4 oligomerization. Together these studies support a unique mode of inhibition in which phenothiazines disrupt the S100A4/ myosin-IIA interaction by sequestering S100A4 via small molecule-induced oligomerization.calcium | X-ray crystallography | NMR | small molecule inhibitor | metastasis T he S100 proteins, of which there are more than 20 members, are characterized by their solubility in 100% saturated ammonium sulfate (1 and 2). Each S100 family member contains two Ca 2þ -binding loops; a C-terminal "typical" EF-hand comprised of 12 residues and an N-terminal pseudo EF-hand consisting of 14 residues. The basic organization of the S100 proteins is a symmetric, antiparallel homodimer, in which the N-and C-terminal helices (helices 1 and 4) from each subunit interact to form a stable four helix bundle that serves as the dimer interface. Calcium binding to the C-terminal typical EF-hand significantly alters the angle between helices 3 and 4, which flank the C-terminal Ca 2þ -binding loop, and exposes a hydrophobic cleft that constitutes a binding surface for target proteins (3-5). Thus the S100 proteins operate as calcium-activated switches that bind and regulate the activity of diverse protein targets. S100 proteins are expressed in a tissue and cell specific manner. Elevated expression of individual family members is associated with a number of human pathologies, including cardiomyopathies, cancer, neurodegeneration, and in...

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“…The solution structure of Prp19p(1-73) was determined using NOE-derived distance constraints and torsion angle constraints derived from chemical shifts using TALOS 28 . Torsion angle dynamics calculations were performed using DYANA 29 , followed by restrained molecular dynamics using AMBER 30 following established protocols [31][32][33] . A summary of structural statistics is provided in Table 2.…”

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confidence: 99%

Structural insights into the U-box, a domain associated with multi-ubiquitination

Ohi

Kooi

Rosenberg

et al. 2003

Nat Struct Mol Biol

262

232

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The structure of the U-box in the essential Saccharomyces cerevisiae pre-mRNA splicing factor Prp19p has been determined by NMR. The conserved zinc-binding sites supporting the crossbrace arrangement in RING-finger domains are replaced by hydrogen-bonding networks in the Ubox. These hydrogen-bonding networks are necessary for the structural stabilization and activity of the U-box. A conservative Val→Ile point mutation in the Prp19p U-box domain leads to premRNA splicing defects in vivo. NMR analysis of this mutant shows that the substitution disrupts structural integrity of the U-box domain. Furthermore, comparison of the Prp19p U-box domain with known RING-E2 complex structures demonstrates that both U-box and RING-fingers contain a conserved interaction surface. Mutagenesis of residues at this interface, while not perturbing the structure of the U-box, abrogates Prp19p function in vivo. These comparative structural and functional analyses imply that the U-box and its associated ubiquitin ligase activity are critical for Prp19p function in vivo.Ubiquitin (Ub) targeting of proteins for degradation by the proteosome involves polyubiquination of substrate proteins via an enzyme cascade consisting of activating (E1), conjugating (E2) and ligating (E3) enzymes. E3 ubiquitin ligases vary widely in size, composition and enzymology, reflecting their regulatory role in substrate recognition 1 . HECT and RING finger domain-containing proteins constitute two classes of E3 ligases. HECT domains bind Ub through a thioester bond and transfer Ub directly to substrate. RING finger E3s facilitate the transfer of Ub from the E2 to the substrate, rather than binding Ub directly.Correspondence should be addressed to K.L.G. kathy.gould@mcmail.vanderbilt.edu or W.J.C. walter.chazin@vanderbilt.edu. 3 These authors contributed equally to this work. Competing interests statementThe authors declare that they have no competing financial interests. HHS Public Access Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptA third class of E3 ubiquitin ligases has been recently identified 2,3 . This class of proteins contains a U-box motif, first identified in Saccharomyces cerevisiae Ufd2p. Ufd2p promotes the elongation of poly-ubiquitin chains in a U-box-dependent manner (recently termed an 'E4' activity) 4 . An alignment of U-boxes and RING motifs indicated that U-boxes lack the strictly conserved histidine and cysteine Zn 2+ -chelating residues found in RING fingers, but they share a similar pattern of hydrophobic and polar amino acids (Fig. 1a), raising the possibility that they have similar folds 5 .S. cerevisiae Prp19p is an essential pre-mRNA splicing factor that contains an N-terminal Ubox 6,7 . Interestingly, a mutation within the Prp19p U-box that results in the substitution of an isoleucine for a conserved valine (prp19-1) leads to pre-mRNA splicing defects and the disruption of several key protein-protein interactions within the spliceosome 8,9 . The profound physiological consequences that result from th...

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The three-dimensional structure of Ca2+-bound calcyclin: implications for Ca2+-signal transduction by S100 proteins

Cited by 123 publications

References 41 publications

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Phenothiazines inhibit S100A4 function by inducing protein oligomerization

Structural insights into the U-box, a domain associated with multi-ubiquitination

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The three-dimensional structure of Ca2+-bound calcyclin: implications for Ca2+-signal transduction by S100 proteins

Cited by 123 publications

References 41 publications

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca2+‐bound closed state: Implications for target recognition

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca2+‐bound closed state: Implications for target recognition

Phenothiazines inhibit S100A4 function by inducing protein oligomerization

Structural insights into the U-box, a domain associated with multi-ubiquitination

Contact Info

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Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition