Báo cáo khoa học: Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon substrate binding pot

Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon substrate binding Urszula Kosinska 1 , Cecilia Carnrot 2 , Michael P. B. Sandrini 3 , Anders R. Clausen 3 , Liya Wang 2 , Jure Piskur 3 , Staffan Eriksson 2 and Hans Eklund 1 1 Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden 2 Molecular Biosciences, Swedish University of Agricultural Sciences, Uppsala Biomedical Centre, Sweden 3 Department of Cell and Organism Biology, Lund University, Sweden Bacillus anthracis and Bacillus cereus are two closely related species of the genus Bacillus. B. anthracis cau- ses anthrax, a disease that in most cases has fatal consequences [1]. B. cereus is a human pathogen asso- ciated with food poisoning [2]. Both species produce endospores under stressful conditions as a means of survival through environmental stress. The major genetic difference between these two species is associ- ated with two toxin-encoding plasmids, pXO1 and pXO2 [3,4], which are present in B. anthracis but not in B. cereus. Thymidine kinase (TK; EC 2.7.1.21) is a deoxyribo- nucleoside kinase (dNK) that phosphorylates thymi- dine to thymidine monophosphate. Mammals possess Keywords deoxythymidine triphosphate; dimer; feedback inhibitor; phosphate donor; tetramer Correspondence H. Eklund, Swedish University of Agriculturla Sciences, Box 590, BMC, Uppsala SE-75124, Sweden E-mail: hasse@xray.bmc.uu.se (Received 28 August 2006, revised 17 November 2006, accepted 24 November 2006) doi:10.1111/j.1742-4658.2006.05617.x Thymidine kinase (TK) is the key enzyme in salvaging thymidine to pro- duce thymidine monophosphate. Owing to its ability to phosphorylate nucleoside analogue prodrugs, TK has gained attention as a rate-limiting drug activator. We describe the structures of two bacterial TKs, one from the pathogen Bacillus anthracis in complex with the substrate dT, and the second from the food-poison-associated Bacillus cereus in complex with the feedback inhibitor dTTP. Interestingly, in contrast with previous structures of TK in complex with dTTP, in this study dTTP occupies the phosphate donor site and not the phosphate acceptor site. This results in several con- formational changes compared with TK structures described previously. One of the differences is the way tetramers are formed. Unlike B. anthracis TK, B. cereus TK shows a loose tetramer. Moreover, the lasso-domain is in open conformation in B. cereus TK without any substrate in the active site, whereas in B. anthracis TK the loop conformation is closed and thymidine occupies the active site. Another conformational difference lies within a region of 20 residues that we refer to as phosphate-binding b-hair- pin. The phosphate-binding b-hairpin seems to be a flexible region of the enzyme which becomes ordered upon formation of hydrogen bonds to the a-phosphate of the phosphate donor, dTTP. In addition to descriptions of the different conformations that TK may adopt during the course of reac- tion, the oligomeric state of the enzyme is investigated. Abbreviations Ba-TK, Bacillus anthracis thymidine kinase; Bc-TK, Bacillus cereus thymidine kinase; Ca-TK, Clostridium acetobutylicum thymidine kinase; dCK, deoxycytidine kinase; dGK, deoxyguanosine kinase; dNK, deoxyribonucleoside kinase; hTK1, human thymidine kinase 1; MPD, 2-methyl-2,4-pentadiol; P-b-hairpin, phosphate-binding b-hairpin; TK, thymidine kinase; Uu-TK, Ureaplasma urealyticum thymidine kinase. FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS 727 four deoxyribonucleoside-specific dNKs: cytosolic deoxycytidine kinase (dCK) and TK1 and mitochond- rial deoxyguanosine kinase (dGK) and TK2. Bacteria, however, have a smaller group of dNKs. Most bacteria have TK that both sequence wise and struc- turally resembles TK1 [5]. In addition, one or two non-TK1-like dNKs can be found in most Gram- positive bacteria. Besides TK, there are two dCK ⁄ dGK-like dNKs in B. anthracis and B. cereus. The amino-acid sequence identity between the TKs from B. anthracis (Ba-TK) and B. cereus (Bc-TK) is as high as 96%. The sequence identity with human TK1 (hTK1) is 37–38%. From amino-acid sequence analysis, it was suggested that dCK, dGK and TK2 belong to one group, which will be referred to as dNKs, whereas TK1-like enzymes form a group of their own. This was confirmed by sub- sequent structure determinations of a multisubstrate Drosophila melanogaster dNK together with human dGK [6], followed by human dCK [7], and later on hTK1 [8,9] and TK from Ureaplasma urealyticum (Uu-TK) [9]. However, Herpes simplex virus type 1 thymidine kinase shares structural and sequential simi- larities with dNKs and does not belong to the TK1- like group of enzymes. dNKs are biological dimers with overlapping substrate specificity, which can be attributed to differences of a few residues in the active site [7,10]. TK1-like enzymes only accept thymidine and deoxyuridine as substrates, and all interactions between the substrate and the enzyme are by main- chain hydrogen bonds to polar groups of the base. The active site of TK1-like enzymes is smaller than that found in dNKs and lined with hydrophobic resi- dues. Whereas TK1-like enzymes have a lasso-domain which covers the active site when the substrate is bound, the active site of dNKs is covered by a helical domain containing an arginine-rich lid. In both enzyme families, the active site is situated at the C-ter- minus of the central parallel b-sheet in the a ⁄ b- domain, which contains a conserved P-loop (GXXXGKS ⁄ T). Yet another difference between dNKs and TK1-like enzymes is the presence of a struc- tural Zn 2+ ion in the lasso-domain of TKs. There are no structural metals in members of the dNK family. Furthermore, all TKs that have been structurally determined form tetramers in the crystals. Enzymes from the dNK and TK1 family can use different NTPs, usually prefer ATP as phosphate donor, and are feedback inhibited by the respective dNTP, such that dTTP is a feedback inhibitor of TK1-like enzymes [11]. It can be concluded that, despite structural differ- ences, dNKs and TKs catalyze the phosphorylation of deoxyribonucleosides in similar ways [9,12]. In this study, we describe the 3D structure of Ba-TK in complex with thymidine and a phosphate ion, as well as Bc-TK with an occupied phosphate donor site. As these enzymes are essentially identical, these structures represent the enzyme trapped in different conforma- tional stages, which reflect structural conformations that TK adopts along its reaction pathway. Results Overall structure TKs from B. anthracis and B. cereus share 96% amino-acid sequence identity. Bc-TK consists of 195 amino acids, and Ba-TK is one amino acid shorter. The last five and the last four amino acids in Bc-TK and Ba-TK, respectively, are different. Besides the dif- ferences in the C-termini, there are only three addi- tional amino acids that are not conserved. The lysine at position 76 in Ba-TK is a glutamic acid in Bc-TK, the methionine at position 82 in Ba-TK is a leucine in Bc-TK, and the alanine at position 147 in Ba-TK is a valine in Bc-TK. These minor differences do not affect the overall structures of Ba-TK and Bc-TK, thus these proteins may be considered structurally identical. The overall structures of Ba-TK and Bc-TK closely resemble previously described TK structures [8,9, 13,14]. The enzymes are tetramers with 222-fold sym- metry and two types of subunit–subunit interaction. One is formed between helices a1 of two neighboring subunits, and the other is between the edges of the b-sheets. The subunit comprises two domains, the N-terminal a ⁄ b-domain and the C-terminal lasso- domain (Fig. 1). The a ⁄ b-domain is formed from a central, six-stranded, parallel b-sheet situated between a long a-helix, a1, and a flexible loop on one side and three shorter helices, a2–a4, on the other side. We have chosen to name the flexible loop, which is about 20–25 residues in length (amino acids 46–68 for Ba-TK and Bc-TK), the phosphate-binding b-hairpin (P-b-hairpin). As previously described [14], the P-b- hairpin is a flexible part of the TK, which has been reported as missing or having a variety of different conformations. There is also a phosphate-binding motif, the P-loop (GXXXXGKS ⁄ T), in the junction between b1 and a1 of the a ⁄ b-domain. The lasso- domain, so called because of its ability to capture and position the substrate [9], comprises two perpendicular b-hairpins, where the longer hairpin opens up to form a lasso-shaped loop. A Zn 2+ ion ligated by four cys- teine residues (Cys145, 148, 183 and 186) stabilizes the lasso-domain. The active site is situated between the a ⁄ b-domain and the lasso-domain. Bacillus thymidine kinase structures U. Kosinska et al. 728 FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS Ba-TK The structure of the Ba-TK–dT complex was refined at 2.7 A ˚ resolution to a final R-factor of 20.3% and R free of 24.4% (Table 1). There is one subunit in the asym- metric unit of the space group I4 1 22. Application of crystallographic symmetries generates the tetramer. The crystal packing creates a mixed, four-stranded b-sheet between the tetramers. The N-terminus and C-terminus from two neighboring subunits of one tetra- mer form a parallel b-sheet, which is connected in an antiparallel manner with the N-terminus and C-termi- nus of a neighboring tetramer. Because of the crystal contacts, it was possible to trace the entire N-terminus as well as two residues from the His-tag. At the C-ter- minus, only the last residue, Arg194, is missing, and Lys192 and Gln193 have flexible side chains which lack electron density. Residues 46–62, which are situ- ated on the P-b-hairpin, also lack electron density and could not be traced. In previously described TK struc- tures, this region was reported to have a variety of conformations or to be missing because of flexibility [14]. As will be described below, this part of the enzyme becomes ordered when the phosphate donor site is occupied. The Ba-TK–dT complex is very similar to the Uu-TK–dT complex [14]. The substrate is bound in a hydrophobic pocket between the a ⁄ b-domain and the lasso-domain, surrounded by Phe92, Leu116, Phe120, Phe125 and Ile170 (Fig. 2A). All hydrogen bonds between the thymine and the enzyme are to main-chain atoms such that O2 and N3 form hydrogen bonds to main-chain atoms of residues in the lasso-domain and O4 to main-chain atoms in the a ⁄ b-domain. The methyl group of thymine points towards Thr155. O3¢ of the deoxyribose makes a hydrogen bond with main- chain nitrogen of Gly174 in the lasso-domain, and O5¢ is hydrogen-bonded to Glu89, which has been sugges- ted to be the catalytic base (Fig. 2B) [9]. Besides strong electron density for dT, there is addi- tional density close to the P-loop which has been inter- preted as a phosphate ion originating from the crystallization buffer. The position of the phosphate corresponds to the c-phosphate of the dTTP molecule bound as feedback inhibitor to hTK1 and Uu-TK [8,9]. The phosphate ion is coordinated by the residues in the P-loop: the side chain of Lys21 and main-chain atoms of residues 18–20. Bc-TK Bc-TK crystallized in the same space group, I4 1 22, as Ba-TK but with different crystal packing and unit cell parameters (Table 1). As in Ba-TK crystals, there is Table 1. Data reduction and refinement statistics. Values in par- entheses refer to outer resolution shell. Ba-TK Bc-TK Space group I4 1 22 I4 1 22 Unit cell parameters (A ˚ )a¼ b ¼ 73.2 c ¼ 223.7 a ¼ b ¼ 95.4 c ¼ 204.9 Resolution (A ˚ ) 2.7 2.8 No. of unique reflections 8799 12035 Multiplicity 14.1 13.6 Completeness (%) 99.9 (99.9) 99.8 (99.8) R meas 10.6 (49.3) 10.0 (53.4) <I⁄ rI > 22.6 (5.9) 26.8 (4.2) Refinement R (%) 20.3 19.6 R free (%) 24.4 23.9 R.m.s.d. bond length (A ˚ ) 0.011 0.011 R.m.s.d. bond angle (°) 1.34 1.48 Average B factors (A ˚ 2 ) a 42.8 57.8 a Average B factor is calculated for residual B factors. Fig. 1. Superposition of subunits of Ba-TK with dT (in green) and Bc-TK with phosphate donor-mimicking dTTP and MPD bound in the thymine-binding pocket (in yellow). The lasso-loop is in closed conformation when dT is present and in open conformation when the substrate is absent. The phosphate donor stabilizes the P-b-hairpin. This part of the molecule is flexible and could not be traced in Ba-TK. U. Kosinska et al. Bacillus thymidine kinase structures FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS 729 one subunit in the asymmetric unit, thus the tetramer is formed after application of symmetry operators. The N-termini of two subunits within the same tetramer form an antiparallel b-sheet. The crystallographic interactions between the tetramers involve only the lasso-domains, which are packed such that the lasso of one tetramer partly covers the lasso of a crystallo- graphically related molecule in another tetramer (sup- plementary Fig. S1). The electron density is continuous from residue 1 through 191. In contrast with Ba-TK, the entire region between residue 46 and 62 is fully traceable, forming a b-hairpin. The formation of the hairpin is mediated by a nucleo- tide binding in the phosphate-binding site. Bc-TK was cocrystallized with the feedback inhibitor dTTP, hence we expected it to bind as thymine in the substrate-bind- ing site between the lasso-domain and a ⁄ b-domain, and the c-phosphate bound to the P-loop as described previ- ously [8,9]. Interestingly, there is no electron density for the inhibitor in the substrate-binding site. Instead, there is strong positive electron density in the phosphate donor site, which is situated opposite the substrate- binding site. It was not possible to conclude from the initial map whether the electron density represented an ATP molecule originating from buffers used during protein purification or a dTTP molecule mimicking a phosphate donor. Consequently, during the early steps of ligand fitting, refinement was carried out with both ATP and dTTP. The electron density corresponding to the ribose moiety was negative at the 2¢-OH position when ATP was used in the refinement, and the size of the electron density for the base was more compatible with a pyrimidine. From this, we concluded that there was a deoxyribonucleoside triphosphate, i.e. a dTTP molecule, occupying the phosphate donor site (Fig. 2B). dTTP can act as a phosphate donor for Ba-TK, but it does so poorly compared with ATP: dTTP is only 3% as efficient as ATP as phosphate donor when dT is used as substrate [15]. An occupied phosphate donor site gives rise to a 3-A ˚ dissociation of subunits interacting by a1. The base of dTTP is inserted between the a1-helix of two subunits and is stacked between the rings of Phe18 and Phe34 from the adjacent subunit (Fig. 2B). These two residues are conserved as hydrophobic residues in all organisms but Gram-negative bacteria where Phe18 is replaced by asparagine and Phe34 is replaced by glutamic acid (Fig. 3). The exchange of hydrophobic residues for polar ones abolishes the hydrophobic stacking interactions between the base and the enzyme. The pattern of interaction of ATP with TKs from Gram-negative bacteria remains to be evaluated. O4 of the thymine makes a hydrogen bond with the main- chain nitrogen of Val144. O3¢ of deoxyribose is hydro- gen-bonded to Glu23, and O4¢ is hydrogen-bonded to His58. The phosphates are stabilized by main-chain nitrogens of P-loop residues as well as by side-chain interactions with Lys21 and Ser22. In addition to the- ses interactions, Ser57 and the main-chain nitrogen from His58, both situated on the P-b-hairpin, also make hydrogen bonds with the phosphates (Fig. 2B). The b-phosphate of dTTP as phosphate donor is very well aligned with the c-phosphate of dTTP bound as a feedback inhibitor, as observed in Uu-TK and hTK1 [8,9]. dTTP not only provides binding partners for resi- dues of the P- b-hairpin, but also affects the interac- tions between subunits of the tetramer. During the refinement and rebuilding process, posit- ive density started to appear in the substrate-binding pocket and was interpreted as a 2-methyl-2,4-pentadiol (MPD) molecule originating from the crystallization solution. The position of the MPD molecule Fig. 2. (A) The active site of Ba-TK is occupied by dT and a phosphate ion. The active site is lined by hydrophobic residues. The map is a Fo-Fc map contoured at 3r (0.1 e ⁄ A ˚ 3 ). (B) The phosphate donor site of Bc-TK with dTTP mimicking the phosphate donor. The base of the phosphate donor is stacked between Phe18 and Phe34 each from adjacent subunits shown in yellow and orange, respectively. The phos- phates are ligated by side-chain and main-chain atoms from the P-loop and P-b-hairpin. The map is a Fo-Fc map contoured at 3r (0.1 e ⁄ A ˚ 3 ). Bacillus thymidine kinase structures U. Kosinska et al. 730 FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS corresponds to the location of thymine of dT or dTTP as observed in Ba-TK with dT, hTK1 with dTTP, and Uu-TK with dT or dTTP (Fig. 1). The oxygens of the MPD molecule form hydrogen bonds to main-chain and side-chain atoms of the residues in the lasso-loop (supplementary Fig. S2). A dNTP molecule can generally bind as a phosphate donor or a bisubstrate inhibitor. Whether it binds in one or the other direction is primarily determined by the affinity of the base of the dNTP for the substrate site. Normally, the preferred bisubstrate inhibitor is the dNTP where the base represents the best substrate. Otherwise, it binds as a phosphate donor. A switch from the bisubstrate situation to the phosphate donor situation can be achieved by competing binding in the substrate site. This was recently shown in a study of deoxyadenosine kinase, where dCTP could be bound as a bisubstrate inhibitor in the absence of substrate but acted as a phosphate donor in the presence of sub- strate [16]. The high concentration of MPD as a pre- cipitant in the crystallization,  2.5 m, had some unexpected consequences. Most surprisingly, it preven- ted the dTTP molecule from binding in its natural site as a bisubstrate inhibitor and instead promoted bind- ing to the phosphate donor site. Although MPD binds with much lower affinity than dTTP, at this high con- centration it is able to compete with dTTP, which is present at about 1000 times lower concentration. The lasso-loop in Bc-TK has a different conforma- tion from that observed in Ba-TK (Fig. 1). In Ba-TK, where dT is occupying the active site, the lasso is closed down over the active site and stabilized by hydrogen bonds to thymidine. The absence of a nat- ural substrate with hydrogen interaction partners, as is the case in the Bc-TK structure, makes the lasso-loop flexible. Because of crystallographic interactions, we were able to trace the entire lasso-loop (supplementary Fig. S1). An open conformation of the lasso-loop is also present in the structure of TK from Clostrid- ium acetobutylicum (Ca-TK) in complex with ADP (PDB code 1XX6) [17]. In the Ca-TK structure, there are neither substrates nor crystal contacts that can pro- vide stabilizing partners. Therefore, parts of the lasso- loop are missing. The presence of an MPD molecule in the substrate site of Bc-TK may also add stabilizing interaction partners for the lasso-loop, but crystal con- tacts are probably more important for this stabiliza- tion. Without such, the lasso-loop might have been as flexible as in Ca-TK. Subunit–subunit interactions There are two types of subunit–subunit interaction in the tetramer. One is between the long a-helices, a1, between adjacent subunits (Fig. 4A). The helices make an antiparallel helix pair with hydrophilic or basic Fig. 3. Amino-acid sequence alignment of the TK1-like enzymes from B. anthracis (AAT57468), B. cereus (DQ384595), C. acetobutylicum (NP_349490.1), U. urealyticum (NP_078433), human (P04183), mouse (NP_033413), Arabidosis thaliana (AAM63086.1), Escherichia coli (NP_415754.1) and Yersinia pestis (NP_405720.1). The secondary-structure elements for Ba-TK and Bc-TK are shown above the alignment. The P-loop and the zinc coordinating motifs are boxed. The catalytic Glu89 is marked in red, and the Phe18 and Phe34, which stack the base of the phosphate donor, are marked in green. Whereas the catalytic base is conserved among TKs from different kingdoms, the stacking phenylalanines are exchanged for hydrophilic residues in Gram-negative bacteria. The residues marked in blue take part in subunit–subunit interactions. U. Kosinska et al. Bacillus thymidine kinase structures FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS 731 residues facing the interaction surface. In the case of Ba-TK, several hydrogen bonds form between side- chain atoms and main-chain atoms of the neighboring helices: NH1 of Arg27 is hydrogen-bonded to main- chain oxygen of Ser19, and NH1 of Arg31 forms a hydrogen bond to the carboxyl oxygen of Phe18. In Gram-negative bacteria, Arg27 and Arg31 are replaced by glutamine and asparagine, respectively (Fig. 3). Despite this change in amino acids, the possibility of forming a hydrogen bond between the two subunits is retained. In Ba-TK, the position of Arg31 is such that ionic interactions between Arg30 and Arg31 with Glu23 are formed. However, in Bc-TK, the distance between the interfacing helices is 3 A ˚ longer than in Ba-TK, and the only subunit–subunit interaction is by hydrogen bonds between NH2 of Arg31 and main- chain oxygen of Gln142 and Ala143 but not with Phe18 as observed in Ba-TK. In the second type of subunit–subunit interaction, the b-sheet of one subunit is attached in an antiparallel way to the b-sheet in the neighboring subunit (Fig. 4B). This subunit interaction predominantly involves residues from strands b6 and helix a4. Val138, which is situated in the middle of the b6 Fig. 4. (A) The subunit–subunit interactions along a1 as observed in Ba-TK (green) and Bc-TK (yellow). The distance between neighboring subunits is  3A ˚ wider in Bc-TK than in Ba-TK. (B) The b-sheet subunit–subunit interactions. In this interaction area, the distance between adjacent subunits is the same for Ba-TK (green) and Bc-TK (yellow). (C) The helical interactions as observed in Bc-TK (yellow) and Ca-TK (grey). Both structures are of the enzymes with occupied phosphate-donor sites, but without substrates. The distance between the adjacent helices is the same in both structures, and the lasso-loops are in open conformation. (D) The superposition of Ba-TK (green), Uu-TK (grey) and hTK1 (black) shows that the helices in adjacent subunits are closer together when the phosphate-donor is absent. In all three enzymes, the lasso-loop is closed down over the active site. Bacillus thymidine kinase structures U. Kosinska et al. 732 FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS strand, is within van der Waals distance of Val138 on the symmetry-related strand. This valine is in some organisms replaced by other hydrophobic residues such as isoleucine or leucine (Fig. 3). At each end of the interaction area, the side chains of Lys140 make hydrogen bonds to main-chain atoms of the neighbor- ing subunits. This lysine is conserved among plants, mammals and Gram-positive bacteria including Myco- bacteria, but replaced with glutamic acid in Gram- negative bacteria. There are also salt bridges between Glu136 and Arg184 from each of the subunits. The salt-bridge formation is conserved among other spe- cies, such that, for hTK1, Glu144 and Arg186 are involved, for Uu-TK, Asp144 and Arg192 are involved, and for Ca-TK, Glu136 and Arg184 make ionic interactions between the side chains. In some organisms, arginine is replaced by lysine. In addition to these interactions, a chain of water molecules is bridged between main-chain atoms of the subunits. The interaction area, calculated as the difference in total accessible surface areas of isolated and interacting structures divided by two [18], formed between b-sheets is larger than that between the a-helices. The b-sheet interactions and the a-helix interactions are 970 A ˚ 2 and 790 A ˚ 2 , respectively, for Ba-TK, and 1030 A ˚ 2 and 413 A ˚ 2 for Bc-TK, when residues 8–45 and 65–187 are used. The a-helical interface area for Bc-TK increases to 550 A ˚ 2 when the P-b-hairpin is included in surface calculations. As a result, binding of the base of the phosphate donor between subunits reduces the subunit–subunit interaction area formed by the a-helices by one third. For comparison, the b-sheet interaction area for hTK1, Uu-TK and Ca-TK is 860–970 A ˚ 2 , and the helical interaction area is 790– 820 A ˚ 2 for hTK1 and Uu-TK and 500 A ˚ 2 for Ca-TK. Thus, the interaction areas for Ba-TK are consistent with the subunit interactions of Uu-TK and hTK1, which, like Ba-TK, have unoccupied phosphate donor sites, whereas contact areas in Bc-TK resemble the contact areas in Ca-TK, which, like Bc-TK, has occu- pied phosphate donor sites and empty acceptor sites. Quaternary structure Our findings regarding the quaternary structure of the Bacilllus TKs called for further studies by other meth- ods. We thus analyzed both enzymes by gel filtration, and, in both cases, obtained only tetramers corres- ponding to a molecular mass of  100 kDa (supple- mentary Fig. S3). Furthermore, we analyzed the enzyme at two different concentrations with dynamic light scattering. In these experiments, Ba-TK at a protein concentration of 3 mgÆmL )1 occurred only as tetramers, whereas the same enzyme at 1 mgÆmL )1 in both the presence and absence of ATP existed as dimers. Bc-TK under all these conditions appeared as dimers (Fig. 5). Discussion In this study, we describe the structures of two homologues, TKs from B. anthracis and B. cereus,in complex with substrate dT and phosphate donor- mimicking dTTP. Because of the high sequence iden- tity between these two enzymes, they can be regarded as the same enzyme at different stages of its reaction. 0 2 4 6 8 10 12 14 16 18 20 22 0.1 1 10 100 Volume (%) Size (r.nm) Size Distribution by Volume A 0 2 4 6 8 10 12 14 16 18 20 22 0.1 1 10 100 Size (r.nm) Volume (%) Size Distribution by Volume B Fig. 5. Size distribution by volume of (A) Ba-TK at a concentration of 3 mgÆmL )1 (red), 1 mgÆmL )1 (green) and 1 mgÆmL )1 +2 mM ATP (blue). The molecular masses calculated from the hydrodynamic radius (4.3 nm for Ba-TK at 3 mgÆmL )1 and 3.2 nm for Ba- TK at 1 mgÆmL )1 +2 mM ATP) are 104 kDa (tetramer) and 51 kDa (dimer), respectively. (B) Bc-TK at a concentration of 3 mgÆmL )1 (red), 1 mgÆmL )1 (green) and 1mgÆmL )1 +2 mM ATP (blue). The molecular mass calculated from the hydrodynamic radius (3.1–3.3 nm for all Bc-TK samples) is 46 kDa, corresponding to a dimer. U. Kosinska et al. Bacillus thymidine kinase structures FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS 733 The lasso-domains of Ba-TK and Bc-TK show a closed and an open form, respectively. In Ba-TK, the lasso-loop is closed down over thymidine and stabil- ized by hydrogen bond donors and acceptors of the substrate, whereas lack of substrate in Bc-TK leaves the lasso-loop flexible. The open conformation of the lasso-domain in Bc-TK resembles the lasso-loop of Ca-TK [17], where part of the loop is missing because of flexibility. In contrast with Ca-TK where the active site is empty and there are no crystallographic interac- tions to stabilize the loop, the lasso of Bc-TK could be fully traced because of stabilizing crystal-packing inter- actions and MPD in the substrate site. The conformation of the P-b-hairpin observed in the Bc-TK structure is similar to that seen in Ca-TK in complex with ADP, Uu-TK in complex with dTTP, and one molecule of Uu-TK in complex with dT [9,14,17]. Together with the lasso-domain, the P-b-hair- pin shields the active site from the solvent. The confor- mations of the P-b-hairpin region observed in subunit A in hTK1 (1W4R) and subunit A in Uu-TK (2B8T) differ significantly from the structures men- tioned above [14]. They may have arisen because of crystal contacts. Nevertheless, lack of electron density or highly diverse conformations when the phosphate donor is absent followed by formation of a b-hairpin in the presence of a phosphate donor indicates that this region of the molecule takes part in the creation of a phosphate donor–acceptor complex. Residues at the tip of the hairpin form hydrogen bonds to the a-phosphate of dTTP bound as phosphate donor. In the literature, TK1-like enzymes have been des- cribed as both dimers and tetramers. The oligomeric state of TK has been studied under various conditions with divergent results [19–23]. In early studies of hTK1 derived from HeLa cells, it was concluded from sedi- mentation in glycerol gradients and gel filtration that hTK1 was a tetramer in solution [23]. Munch-Petersen et al. [22] showed that tetramerization at low protein concentration was an ATP-dependent process in which incubation of hTK1 with ATP reversibly shifted the oligomeric state from a dimer to a tetramer. A recent study of the quaternary state of hTK1 demonstrated that the oligomeric state of wild-type hTK1 is tetra- meric, whereas the N-terminal and C-terminal trun- cated mutant was a dimer irrespective of the concentration and incubation with dT ⁄ ATP [19]. Furthermore, Uu-TK was found as dimers in solu- tion [21]. To investigate if the enzyme could be found as dimers and tetramers, we performed further experi- ments with the Bacillus enzymes. Earlier gel-filtration studies have shown that Ba-TK occurs as dimers [15], whereas the oligomeric state for Bc-TK had not been determined. Our gel-filtration studies of both enzymes demonstrated that both were in the tetrameric state only (supplementary Fig. S3). This is surprising as the conditions in the present and earlier experiments were similar. However, the salt and protein concentrations differ somewhat. We also investigated the enzyme with dynamic light scattering methods. The results in this case were as puzzling as the gel-filtration studies. In only one case, Ba-TK at 3 mgÆmL )1 , did the enzyme occur as tetra- mers. In all other cases, we obtained dimers. The pres- ence of ATP did not influence the quaternary structure. However, the available TK structures, including truncated hTK1, are tetramers with comparable sub- unit–subunit interactions. These results suggest that TK exists as both dimers and tetramers. In solution, the two forms may be in equilibrium, which in crystal- lization conditions, with high protein concentrations and small volumes, is shifted towards the tetrameric form. The observation that, in Bc-TK, the base of dTTP in the phosphate donor position is inserted between two subunits implies that the enzyme was in the dimeric form before the formation of the tetramer and that it can be stable in both states. As mentioned above, all tetramers found in the crys- tal structures are comparable. This study reveals one major difference. Empty phosphate donor sites make it possible for the subunits to form tight tetramers, whereas, when the phosphate donor sites are occupied, as in Bc-TK, the subunits interacting with the long a1 helix are not able to come as close together to make the tight tetramer. On the other hand, the base of the phosphate donor, which is stuck between two subunits, contributes to the subunit–subunit interaction and helps to create the tetrameric state of the enzyme. However, we are not able to determine in this study whether the phosphate donor induces separation of a tetramer formed earlier or if it prevents formation of a tight tetramer. Is the observed position of the phos- phate donor with the base inserted between the sub- units the physiological one? If the enzyme acts as a dimer, it seems likely. However, for a tetramer, separ- ation into dimers to allow insertion of the base would be unfavorable. Moreover, we would like to establish whether it is possible from structural data to determine which of the subunit–subunit interactions is the most stable. In contrast with Birringer et al. [8], we believe that dimers with the b-sheet interaction area are the ones that are observed in solution. There are a number of structural indications that support this conclusion. The interac- tion area formed between the b-sheets is larger than the one formed between the long a-helices and includes Bacillus thymidine kinase structures U. Kosinska et al. 734 FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS conserved salt-bridge interactions, which together with water molecules hydrogen-bonded between the two sheets, make strong contacts. As described above, binding of the phosphate donor does not alter the b-sheet interaction, but significantly decreases the a-helical interaction area. This has also been observed in the structure of Ca-TK complexed with ADP [17], but not in any other TK structure with unoccupied phosphate-donor-binding sites. A longer distance between the adjacent a1-helices is necessary for the base of the phosphate donor to have space to fit between Phe18 and Phe34. Yet another indication that the b-sheet interaction is the most stable one comes from the Uu-TK structure. In contrast with hTK1, the structure of Uu-TK was determined for the full-length enzyme where the C-terminus forms an a-helix, which makes hydrophobic interactions with a2 and a3 of the neighboring subunit in the b-sheet interaction dimer. This increases the interaction area from 870 A ˚ 2 to 2040 A ˚ 2 . Formation of an a-helical dimer as suggested by Birringer et al. [8] would leave the hydrophobic pat- ches of the C-terminal helix unshielded. To conclude, we have described the structures of two almost identical TKs showing open and closed conformations with respect to phosphate acceptor and donor sites. This study shows that an empty TK adopts an open form with two flexible parts. When the substrate, feedback inhibitor, and phosphate donor are all not bound to the enzyme, both the lasso-loop and the P-b-hairpin are flexible. The lasso-loop acts as a lid and traps the substrate or the inhibitor, whereas the P-b-hairpin plays a part in the positioning of the phos- phate donor. Moreover, we have illustrated that the tetramer formed in the presence of the phosphate donor is weaker than that observed in TKs with empty phosphate-binding sites. Experimental procedures Protein expression and purification The B. anthracis Sterne strain (34F2) tk gene was cloned into the pCRÒ4-TOPO vector, subcloned into the pET-14b expression vector and transformed into the chemically com- petent Escherichia coli strain, BL21(DE3) pLysS (Novagen, Madison, WI, USA). Recombinant Ba-TK, fused with an N-terminal His 6 -tag, was expressed by induction with iso- propyl b-d-thiogalactoside and purified by metal ion affin- ity chromatography (HisBind; Novagen) as previously described [15]. The buffers were changed to 20 mm Tris ⁄ HCl (pH 7.6) ⁄ 150 mm NaCl ⁄ 2mm MgCl 2 ⁄ 5mm di- thiothreitol ⁄ 10% glycerol on a PD10 desalting column (GE Healthcare, Uppsala, Sweden). The tdk gene from B. cereus (GenBank accession No. DQ384595) was cloned into the pGEX-2T vector (GE Healthcare) and expressed in E. coli KY895 [24]. Recombin- ant N-terminal glutathione S-transferase (GST)-tagged Bc-TK fusion protein was expressed by induction with iso- propyl b-d-thiogalactoside and subsequently purified on a glutathione–Sepharose FF column (GE Healthcare). Cell- free extract prepared by French Press, centrifugation (Sor- vall RC5 centrifuge, SA-600 rotor, 30 min at 24 500 g) and filtering was loaded on the column, and unbound proteins eluted with buffer A (NaCl ⁄ P i pH 7.3, 10% glycerol, 0.1% Triton X-100). Then one column volume 10 mm ATP ⁄ MgCl 2 in buffer A was circulated over the column for 1 h at room temperature and washed through with buffer A. Finally, one column volume 50 UÆmL )1 thrombin in buf- fer A was loaded on the column before it was incubated at room temperature for 16 h. Pure Bc-TK without the GST- tag was then eluted from the column with buffer A while uncleaved fusion protein and GST-tag remained on the col- umn for elution with glutathione. The protein was further purified on a SuperdexÔ200 HiLoadÔ16 ⁄ 60 prepgrade (GE Healthcare). The buffer used was 10 mm Tris ⁄ HCl (pH 7.6) ⁄ 150 mm NaCl ⁄ 5mm MgCl 2 ⁄ 5mm dithiothreitol. Determination of quaternary structure with dynamic light scattering Three samples of different concentration with and without ATP were prepared of each Bacillus TK. The concentra- tions were 3 mgÆmL )1 TK, 1 mgÆmL )1 TK and 1 mgÆmL )1 TK with 2 mm ATP. The buffer was 20 mm Tris ⁄ HCl (pH 7.6) ⁄ 150 mm NaCl ⁄ 5mm MgCl 2 ⁄ 5mm dithiothreitol. The samples were incubated for 8 h at 4 °C before the measurements. All measurements were performed at 4 °C with a Malvern Instruments (Uppsala, Sweden) dynamic light scattering instrument. Crystallization, data collection and structure determination Ba-TK (10 mgÆmL )1 ) was cocrystallized with dT (5 mm). The crystals grew in hanging drops at 14 °C in 5–24% (depending on the type of crystallization plate) 1,2-pro- panediol, 0.1 m sodium ⁄ potassium phosphate (pH 6) ⁄ 10% (v ⁄ v) glycerol. The data were collected at the European Synchrotron Radiation Facilities (ESRF), Grenoble, France. No cryo-protectant was used before freezing in liquid nitrogen. Data were processed with Mosflm and Scala in CCP4 [25]. The search model for molrep [26] was a polyalanine chain of one subunit of Uu-TK (1XMR or 2B8T) with residues 50–67, 84–88 and 199–217 excluded because of structural flexibility and sequential dissimilarity. One Ba-TK subunit was found in the asymmetric unit. Simulated annealing was U. Kosinska et al. Bacillus thymidine kinase structures FEBS Journal 274 (2007) 727–737 ª 2006 The Authors Journal compilation ª 2006 FEBS 735 performed in cns [27], with further refinement and model building performed with refmac5 [28] and o [29], respect- ively. During the end of the refinement, translation libera- tion and screw rotation displacement (TLS) refinement was applied with all residues forming one TLS group. Twenty water molecules were included. Statistical analysis of data processing and refinement are reported in Table 1. The coordinates have been deposited with PDB code 2J9R. Bc-TK (10–15 mgÆmL )1 ) was mixed with dTTP (5 mm) before crystallization setup. Equal volumes of protein solu- tion were mixed with crystallization solution consisting of 55–65% MPD and 0.1 m Hepes, pH 7.0. Bipyramidal crys- tals grew using hanging drop vapor diffusion at 4 ° C. No cryo-protecting agent was used, and the crystals were fro- zen in liquid nitrogen directly from crystallization drops. The data were collected at ESRF. Indexing and scaling were performed with Mosflm and Scala in CCP4 [25]. Molecular replacement calculations were performed with molrep [26] using one subunit of Ba-TK as search model. As in the case of Ba-TK, there was only one subunit of Bc-TK occupying the asymmetric unit. Cycles of model building, restrained refinement, and TLS refinement were performed in o [29] and refmac5 [28], respectively. Twenty water molecules were included in the final structure. Data collection and refinement statistics are presented in Table 1. The structure has been deposited with PDB code 2JA1. The sequence alignment was performed in clustalw [30], and the figure was made in alscript [31]. The figures pre- senting the protein structures were made with pymol [32]. Acknowledgements This work was supported by grants from the Swedish Research Council for Environment, Agricultural Sci- ences and Spatial Planning (to LY and SE), the Swe- dish Research Council (to HE, JP and SE) and the Swedish Cancer Foundation (to HE). References 1 Dixon TC, Meselson M, Guillemin J & Hanna PC (1999) Anthrax. 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Detection of protein assemblies in crystals Lecture Notes in Computer Science: Computational Life Sciences: Proceedings of the First International Symposium, Complife2005, Konstanz, Germany, September 25–27, 2005 3695, 163–174 19 Birringer MS, Perozzo R, Kut E, Stillhart C, Surber W, Scapozza L & Folkers G (2006) High-level expression and purification of human thymidine kinase 1: quaternary structure, ... contacts stabilize the lasso-loop Fig S2 MPD binding in the phosphate acceptor site of Bc-TK Fig S3 (A) Size-exclusion chromatography of Ba-TK on Superdex 200 10 ⁄ 300 (B) Size-exclusion chromatography of Bc-TK on Superdex 200 16 ⁄ 60 (C) A typical chromatogram of Bc-TK run on Superdex 200 16 ⁄ 60 This material is available as part of the online article from http://www.blackwell-synergy.com Please... JS, Kuszewski J, Nilges M, Pannu NS, et al (1998) Crystallography & NMR system: a new software suite for macromolecular struc- Bacillus thymidine kinase structures 28 29 30 31 32 ture determination Acta Crystallogr D Biol Crystallogr 54, 905–921 Murshudov GN, Vagin AA & Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr D Biol Crystallogr 53, 240–255... Cowan SW & Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr 47, 110–119 Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG & Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res 31, 3497–3500 Barton GJ (1993) ALSCRIPT: a tool to format multiple... Superdex 200 16 ⁄ 60 This material is available as part of the online article from http://www.blackwell-synergy.com Please note: Blackwell Publishing is not responsible for the content or functionality of any supplementary materials supplied by the authors Any queries (other than missing material) should be directed to the corresponding author for the article FEBS Journal 274 (2007) 727–737 ª 2006 The . Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon. describe the structures of two homologues, TKs from B. anthracis and B. cereus, in complex with substrate dT and phosphate donor- mimicking dTTP. Because of the