The Linker of Des-Glu84-Calmodulin Is Bent (Calcium/Mutagenesis/Flexible Tether/Bent A-Helix/Crystallography) S
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Proc. Natl. Acad. Sci. USA Vol. 90, pp. 6869-6873, July 1993 Biochemistry The linker of des-Glu84-calmodulin is bent (calcium/mutagenesis/flexible tether/bent a-helix/crystallography) S. RAGHUNATHAN*, R. J. CHANDROSSt, B.-P. CHENG*t, A. PERSECHINI*§, S. E. SOBOTTKAt, AND R. H. KRETSINGER* Departments of *Biology and tPhysics, University of Virginia, Charlottesville, VA 22901 Communicated by William N. Lipscomb, April 1, 1993 ABSTRACT The crystal structure of a mutant calmodulin 111111111122 22222222 (CaM) lacking Glu-84 has been refined to R = 0.23 using data 123456789 012345678901 23456789 measured to 2.9-A resolution. In native CaM the central helix domain n nn n X Y Z(Y) X Z n nn n is fully extended, and the molecule is dumbbell shaped. In contrast, the deletion of Glu-84 causes a bend of 950 in the 1 ADQLTEEQIA EFKEAFSLF DKDGDGTITTKE LGTVMRSL39 linker region of the central helix at Ile-85. However, EF-hand 2 GQNPTEA ELQDMINEV DADGNGTIDrPz rLTMKARKP75 domains 1 and 2 (lobe 1,2) do not touch lobe 3,4. The length, by a-carbon separation, of des-Glu5"-CaM is 56 A; that of 3 76MKDTDSEE EIRZAFRVr DKDGNGYISAAE LRHVMTNL112 native CaM is 64 A. The shape of des-Glu"-CaM is similar to 4 GEKLTDE EVDEMIREA DIDGDGQVNYEE FVQMMTAK148 that ofnative CaM, as it is bound to the target peptide ofmyosin light-chain kinase. This result supports the proposal that the FIG. 1. The amino acid sequence ofvertebrate CaM is aligned by linker region of the central helix of CaM functions as a flexible its four EF-hand domains, each consisting of 29 residues. The side tether. chains whose oxygen atoms coordinate calcium are aligned under X, Y, Z, -X, -Z. The carbonyl oxygen of (-Y) coordinates calcium with its peptide oxygen. The insides ofa-helices E and F usually have Calmodulin (CaM) is the most extensively studied of the 30 hydrophobic side chains, indicated by n. The central helix consists subfamilies (1) that contain two to eight EF-hand domains. It of the second (F) helix of domain 2, the eight-residue linker 76-83, regulates numerous target enzymes and structural proteins and the first (E) helix ofdomain 3. Glu-84, the first residue ofdomain (2) and is inferred to be present in all cells of all eukaryotes. 3, is shown in italics as the residue deleted in des-Glu4-CaM. The We want to understand the mechanisms whereby CaM trans- region Lys-77-Thr-79 is predicted not to be helical. Native CaM with duces the information in a pulse of Ca2+ ions in the cytosol three glutamates has a slightly stronger helix-forming tendency than to a change of conformation of a target enzyme. To this end does des-Glu84-CaM with only two adjacent glutamates. There is a Persechini and Kretsinger (3) made three mutant CaMs in bend of 950 in the helix centered about Ile-85 and a bend of 40' at which the linker region of the central helix has one (des- Lys-75 in des-Glu"-CaM. Glu84-CaM), two (des-Glu83, Glu4-CaM), or four (des-Ser8l, range 3.1-2.9 A the redundancy is 2.1, the mean I/ar is 5.3, Glu82, Glu83, Glu84-CaM) residues deleted. Persechini et al. and the scaling residual is 0.115. (4) treated mutated CaM (Gln-3 -3 Cys, Thr-146 -) Cys) with bismaleimidohexane to cross-link this mutated CaM into a Given the difficulty of growing larger crystals and the bent form. On the basis ofthe abilities ofthese deletion CaMs assumed similarity in structure of native CaM and of des- to activate skeletal muscle myosin light-chain kinase Glu84-CaM, we computed self-rotation and molecular replace- (skMLCK), NAD kinase, and calcineurin (protein phospha- ment functions. We routinely describe the EF-hand domain in tase) and of the cross-linked CaM to activate skMLCK, they terms of 29 residues, as illustrated in Fig. 1 and explained in proposed "that the central helix of calmodulin functions as a its legend. The four canonical domains of CaM extend from flexible tether." residue 11 through 39, 47-75, 84-112, and 120-148. We anticipated that des-Glu84-CaM would have four EF-hand EXPERIMENTAL PROCEDURES domains with domains 1 and 2 related by an approximate 2-fold Des-Glu4-CaM was prepared, as described by Persechini rotation axis forming lobe 1,2, very similar to those observed and Kretsinger (3), and was crystallized by vapor distillation in native CaM and troponin C (TnC). Lobe 3,4 should also from drops over reservoirs of 20%o saturated ammonium consist ofa pair of EF-hands related by an approximate 2-fold sulfate/10 mM CaCl2/50 mM 2-(N-morpholino)ethanesulfo- rotation axis. We hoped to determine the rotation operation nic acid, pH 6.1, at both 4°C and 20'C. Initial drops consisted relating lobe 1,2 to lobe 3,4. We found a single rotation axis in of 8.0 ,ul of des-Glu84-CaM at 10 mg/ml and 8.0 ,ul of the self-rotation function with the rotation value K 1800. We reservoir. Our largest crystals seldom exceeded 0.25 mm in could interpret this result only in terms of the subsequent any dimension; diffraction was weak beyond 2.9 A. Unit cell molecular replacement calculations. dimensions and intensity data were measured at the Multi- Molecular replacement searches were computed by using wire Area X-ray Diffractometer Facility (5). Systematic the package CCP4 (6). We used lobe 1,2 (residues 11-75) and absences indicate space group P212121 with unit cell dimen- lobe 3,4 (84-147) as probes (probe 1,2 and probe 3,4). The sions a = 45.3, b = 49.9, c = 62.4 A; one molecule per results were relatively insensitive to the exact definition of asymmetric unit. The 3396 unique reflections of 3483 avail- probe termini as well as to both radius of integration and able reciprocal lattice points were measured to a resolution of resolution of data used. On the basis of several preliminary 2.9 A. The redundancy ofmeasurements is 3.8. The mean I/oa trials we used 20-A radius, 10- to 4-A data, and all nonhy- is 6.6; 2371 reflections have I/cr > 3.0. The overall scaling residual - I,I/n is 0.09. In the resolution Abbreviations: CaM, calmodulin; TnC, troponin C; skMLCK, skel- Y:.=j[7,jgi(Iji Ijj)/m etal muscle myosin light-chain kinase. *Present address: Institute of Solid State Physics, Academia Sinica, The publication costs of this article were defrayed in part by page charge Hefei, People's Republic of China. payment. This article must therefore be hereby marked "advertisement" §Present address: Department of Physiology, School of Medicine, in accordance with 18 U.S.C. §1734 solely to indicate this fact. University of Rochester, Rochester, NY 14642. 6869 Downloaded by guest on September 26, 2021 6870 Biochemistry: Raghunathan et al. Proc. Natl. Acad Sci. USA 90 (1993) drogen atoms. In cross-rotation functions probe 1,2 gave rotation peaks). As anticipated, the resulting maps were very three significant peaks (Fig. 2A), and probe 3,4 gave two of noisy because each search used only halfofthe molecule. We the three (Fig. 2B). Similar results were obtained when atoms then used each of several solutions to the translation function beyond the (3-carbon were omitted, the polyalanine model. for probe 1,2 as a fixed contribution, while we searched for Because the two lobes of CaM are so similar, it was expected the translation component of probe 3,4 and vice versa. We that both probes would give the same two peaks, one found only one rotation, translation solution for probe 1,2 corresponding to the 1,2 lobe of des-Glu84-CaM and one that gave a significant solution for probe 3,4 and conversely corresponding to lobe 3,4. We could not, however, at this only one rotation, translation solution for probe 3,4 that gave point determine which search peak corresponded to which a significant solution for probe 1,2 (Fig. 2 C and D). lobe of des-Glu4-CaM. At this point we had tentatively identified the correct We computed translation functions for both cross-rotation rotation and translation matrices for probe 1,2 and for probe function solutions (and as a control for several smaller 3,4 but did not know which corresponded to lobe 1,2 of A CROSS ROT PROBE 1,2 B CROSS ROT PROBE 3,4 -6C 1800 0 I~~so at 180 JR 7 360 360 a = 75, 80, 85 & 90 = 85&90 C D ci; tOSS TRANS FIX 3,4 PROBE 1,2 CROSS TRANS FIX 1,2 PROBE 3,4 ' Z 0.5 0 Z 0.5 v X --I= ocr 0.5 0.5 Y = 0.214, 0.228, 0.242, 0.256 & 0.270 Y = 0.343, 0.357, 0.371 & 0.385 FIG. 2. Molecular replacement calculations using both lobe 1,2 and lobe 3,4 ofnative CaM as probes revealed the orientations and translations of the two lobes of des-Glu84-CaM. The radius of integration is 20 A; data from 10-4 A are used. (A) Cross-rotation (CROSS ROT) function computed including all side chains of residues 11-75 (lobe 1,2) of native CaM as probe. The map is computed at 19 intervals of , from 00 through 900. Contours are drawn at 3.6 times the mean level, exclusive of the origin peak, and are displayed, in superposition, for levels i3 = 750, 800, 850, and 900.