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1 Department of Applied Chemistry and 2 Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
Reprint requests to: Yasushi Kai, Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan; e-mail: kai{at}chem.eng.osaka-u.ac.jp; fax: +81-6-6879-7409.
(RECEIVED August 17, 2005; FINAL REVISION October 14, 2005; ACCEPTED October 14, 2005)
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structure, in which three -helices enclose the central -sheet. The topology of this domain is similar to that of holliday junction resolvase Hjc from Pyrococcus furiosus. The C-terminal domain comprises three -helices, six -strands, and two 310-helices. In the dimer structure of Tk-TIP26, two molecules are related with the crystallographic twofold axis, and these molecules rigidly interact with each other via hydrogen bonds. The complex of Tk-TIP26/Tk-TBP is isolated and analyzed by SDS-PAGE and gel filtration column chromatography, resulting in a stoichiometric ratio of the interaction between Tk-TIP26 and Tk-TBP of 4:2, i.e., two dimer molecules of Tk-TIP26 formed a complex with one dimeric TBP. The electrostatic surfaces of Tk-TIP26 and TBP from Pyrocuccus woesei (PwTBP) allowed us to build a model of the Tk-TIP26/TBP complex, and to propose the inhibition mechanism where two dimer molecules of Tk-TIP26 bind to a dimeric TBP, preventing its binding to TATA-DNA. Keywords: transcription; TATA-binding protein (TBP); TBP-interacting protein; hyperthermophilic archaeon; X-ray crystallography; Cys2–His2 type zinc finger motif; gel filtration chromatography; protein structure/folding; structure/function studies; protein crystallization; docking proteins
Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051788906.
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homolog (TFE), and TFE could play a stimulatory role in transcription initiation (Bell and Jackson 2001; Bell et al. 2001a, b; Hanzelka et al. 2001). These results suggested that archaeal transcription shares high degrees of similarity with that of eukarya, and that it is simpler than eukaryal transcription. This simplicity of archaeal transcription could be a prototype in order to increase our understanding of eukaryotic transcription mechanisms. To further our understanding of transcription mechanisms, it is very important to understand transcription factors other than GTFs. Recent studies suggested that several new transcription factors could interact with TBP. Some of them are referred to as "TBP-interacting proteins" (TIPs) because they were isolated using the affinity chromatography with TBP (Makino et al. 1996). TIPs have been identified in both eukaryal and archaeal cells. In eukarya, the most studied TIPs are TIP120 (Yogosawa et al. 1996) and TIP49 (Kanemaki et al. 1997). TIP120 was isolated from rat liver, and sequence analyses showed that the N-terminal region of TIP120 exhibited 44% of sequence similarity to that of Drosophila TAF80 (Yogosawa et al. 1996). Kinetic studies and electrophoretic mobility shift assays showed that TIP120 activated the basal levels of transcription from various kinds of promoters and also stimulated the DNA-binding activity of RNA polymerase II (Makino et al. 1999). TIP49 was also isolated from rat liver nuclear extracts using the affinity chromatography with TBP. The amino acid sequence of TIP49 contains an ATP-/GTP-binding P-loop, and exhibits sequence similarity of bacterial DNA helicase RuvB (Yamada et al. 2001). In archaea, eukaryal TIP49 homologs were identified in the genomes of Archeaoglobus fulgidus and Pyrococcus horikoshii (Soppa 1999). TIP26 was also isolated and characterized in several species of Thermococcales (Matsuda et al. 1999).
In 1999, Matsuda et al. first identified TIP26 in the Thermococcus kodakaraensis strain KOD1 (Tk-TIP26). KOD1 was isolated from a solfatara at a wharf on Kodakara Island, Kagoshima, Japan. The growth temperature of this strain ranges from 65° to 100°C, with an optimal growth temperature of 95°C (Morikawa et al. 1994; Fujiwara et al. 1998). Tk-TIP26 was isolated from cell lysates of this strain by affinity chromatography with TBP-agarose (Matsuda et al. 1999). Cloning of the gene encoding this protein showed that Tk-TIP26 is composed of 224 amino acid residues (molecular weight 25,558), and exists in a dimeric form. Database analyses indicate that the orthologous genes are only present in the genomes of two genera, Pyrococcus and Thermococcus. The recombinant Tk-TIP26 and Tk-TBP interact with each other with an equilibrium dissociation constant, KD, of 1.24–1.46 µM (Matsuda et al. 1999). Further studies on this protein revealed that in the absence of Tk-TFB, Tk-TIP26 prevents Tk-TBP from binding to TATA-DNA (Matsuda et al. 1999). On the other hand, in the presence of Tk-TFB, Tk-TIP26 does not inhibit the formation of the TFB/TBP/TATA-DNA ternary complex but interacts with this complex to form the TIP26/TFB/TBP/TATA-DNA quaternary complex (Matsuda et al. 2001). These results suggest that TIP26 plays a role as a new possible transcription regulation factor in Thermococcales.
Biological or biochemical studies have identified and characterized TIPs, but no three-dimentional structures of TIPs have been determined, while this information is required for further understanding of the interaction between TIPs and TBP.
We report here the first crystal structure of TBP-interacting protein (Tk-TIP26) from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. In addition, we report the isolation of the Tk-TIP26/Tk-TBP complex. Characterization of this complex, and structural information about Tk-TIP26 and archaeal TBP gave us the insights on molecular mechanism of the interaction between TIP26 and TBP.
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-helices (a1–a7), 12 -strands (b1–b12), and 2 310-helices (A1 and A2), with overall dimensions of 64 x 49 x 28 Å (Fig. 1A
). Additional electron densities derived from a part of a histidine tag (his-tag) are located before Met1. The last five residues of the his-tag (Pro5, Arg4, Gly3, Ser2, and His1) and the first three residues of Tk-TIP26 (Met1, Tyr2, and Ala3) form -helix "a1" (Fig. 1A,B). Side residues of Arg4 and Ser2 form hydrogen bonds with those of Glu109 and Arg188 in the counterparts of the symmetrically equivalent molecules, respectively. Previously, we obtained the crystals of Tk-TIP26 without the his-tag. However, they diffracted to only 3.2 Å or worse, and they were not isomorphous (data not shown). The intermolecular interactions derived from the his-tag could contribute to the packing stabilization of molecules in the crystal and the improvement of resolution limit.
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N-terminal domain of Tk-TIP26
The N-terminal domain of Tk-TIP26 comprises four -helices (a1–a4) and six -strands (b1–b6), forming an / structure, in which the central -sheet, formed by six -strands, is surrounded by three -helices: a2, a3, and a4 (Fig. 2A). As mentioned above, the folding of the N-terminal domain of Tk-TIP26 is similar to that of proteins with the topology of type II restriction endonucleases. Among these, archaeal holliday junction resolvase Hjc from Pyrococcus furiosus (Pfu-Hjc; PDB ID 1GEF
[PDB]
; Nishino et al. 2001a, b) is the most topologically similar (Fig. 2A,C). Interestingly, the superimposition between the N-terminal domain of Tk-TIP26 and monomeric Pfu-Hjc shows an RMSD value for C carbon atoms of 3.5 Å , even though their sequence similarity is <10%. However, the electrostatic surface of the N-terminal domain of Tk-TIP26 is remarkably different from that of Pfu-Hjc. The N-terminal domain of Tk-TIP26 is mainly negatively charged, while Pfu-Hjc is positively charged (Fig. 2B). In addition, the arrangements of Tk-TIP26 in the dimer are notably different from that of Pfu-Hjc (Nishino et al. 2001a,b). Tk-TIP26 forms a dimer via the interaction between the N-terminal domain and the C-terminal domain in the counterpart of the dimer (Fig. 4A, below), while Pfu-Hjc is dimerized with a single domain. The contact of the dimeric -TIP26 involves hydrogen bonds (see below), while that of Pfu-Hjc involves hydrophobic interaction (Nishino et al. 2001a,b). These results suggest that Tk-TIP26 does not have the same function as in Pfu-Hjc, even though these two proteins share similar topology.
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-helices (a5–a7), six -strands (b7–b12), and two 310-helices (A1 and A2). A zinc ion is found in the vicinity of the loop region between b9 and b10 (Fig. 3). The ion is coordinated by two cysteine (Cys149 and Cys152) and two histidine residues (His164 and His168), forming a tetrahedral coordination architecture. The secondary structures around these four residues are composed of -strands b9 (from Tyr140 to Lys147), b10 (from Tyr154 to Asp156), and -helix a6 (from Leu160 to Arg165), forming the classical Cys2His2-type zinc finger motif.
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-hairpin and an -helix. The zinc finger motif in Tk-TIP26 is an unusual Cys2His2-type zinc finger and is not functional as a DNA-binding module, probably because Tk-TIP26 possesses only a single zinc finger motif. Zinc finger proteins usually contain multiple zinc finger motifs, which are required for specific interaction with DNA (Pavletich and Pabo 1991). In addition, this motif should not have the critical role for the stability of overall structure, because its mutant protein C149A/C152A could be over-expressed and purified as in wild-type protein (Matsuda et al. 1999).
This zinc finger motif is the first structure of Cys2His2-type zinc finger motif among archaeal proteins. However, the role of the motif in Tk-TIP26 is not unknown, and should be elucidiated.
Dimer structure of Tk-TIP26
Previously, it was reported that Tk-TIP26 exists in a dimeric form (Matsuda et al. 1999). The structure of dimeric Tk-TIP26 is shown in Figure 4A
. Two molecules of Tk-TIP26 are related by the crystallographic twofold axis and the contact surface area is calculated to be 2260 Å2. The dimer interface is mainly composed of the -strands b1 and b8 in the counterpart of the dimer (Fig. 4B,C). The contact involves hydrogen bonds between side residues of Lys37, Tyr120, Asp118, and Lys113 in one molecule, and Asp21, Asp20, Lys36, and Glu25 in the other, respectively. Hydrogen bonds are formed between main chains of Gln116 and Leu114 in one molecule, and Trp24 and Ile26 in the other, respectively (Fig. 4B,C).
Formation of a Tk-TIP26/Tk-TBP complex
Purified Tk-TIP26 and Tk-TBP were mixed and incubated at 303 K for 30 min. After incubation, this mixture was applied to gel filtration column chromatography to purify. The chromatograph shows a single peak with molecular weight of ~158 kDa, showing that a Tk-TIP26/Tk-TBP complex is obtained (Fig. 5A). This value is in agreement with an estimate of molecular weight of this complex using dynamic light scattering (DLS) (data not shown). The peak fraction was applied to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The resultant gel shows just two bands (Fig. 5B): one derived from Tk-TIP26 (molecular mass of ~27 kDa), and the other, from Tk-TBP (molecular mass of ~23 kDa). For the estimation of the stoichiometry of the interaction between Tk-TIP26 and Tk-TBP, several concentrations of Tk-TIP26, Tk-TBP, and the Tk-TIP26/Tk-TBP complex were loaded to SDS-PAGE on the same gel. The resultant gel was analyzed for band intensities in order to produce calibration curves of Tk-TIP26 and Tk-TBP (data not shown). The calibration curves indicate that in the lane of the Tk-TIP26/Tk-TBP complex, 0.126 pmol of Tk-TIP26 and 0.0675 pmol of Tk-TBP were present, i.e., the molar ratio of the interaction between Tk-TIP26 and Tk-TBP is ~2:1. Together with the estimation of molecular weight of the Tk-TIP26/Tk-TBP complex, Tk-TIP26 and Tk-TBP interact with stoichiometry of 4:2.
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Inhibition of the interaction between TBP and TATA-DNA by Tk-TIP26
In the absence of Tk-TFB, Tk-TIP26 prevents Tk-TBP from binding to TATA-DNA (Matsuda et al. 1999, 2001). We compared the structures and the electrostatic surfaces of Tk-TIP26 and TBP from Pyrococcus woesei (DeDecker et al. 1996) (PwTBP; PDB ID 1PCZ
[PDB]
), which shares 83% of amino acid similarity with Tk-TBP. In the structure of dimeric Tk-TIP26, a negatively charged cleft is formed after formation of the dimer (Fig. 6A, left). On the other hand, dimeric TBP possesses specifically positively charged surfaces composed of Arg78, Lys82, Lys86, Lys88, Lys93, and Lys95 on both ends of the surface of the dimeric PwTBP (Fig. 6A, right). Subsequently, a model of the Tk-TIP26/TBP complex was predicted (Fig. 6B). In this model, dimeric TBP is sandwiched by two molecules of dimeric Tk-TIP26 from both ends of the surface, forming a 4:2 complex. Recent studies suggested that the equilibrium between TIP26/TBP complex and TBP/TATA-DNA complex inclines toward the fraction of the former complex in the absence of TFB(Matsuda et al. 2001). In addition, the 4:2 complex cannot access TATA-DNA in the absence of TFB (Matsuda et al. 1999), while dimeric TBP can interact with TATA-DNA by the dissociation to monomers (Coleman et al. 1995). These results suggest that the formation of the 4:2 complex would stabilize TBP in dimeric form, although it has not been elucidated how the interaction between the monomers of dimeric TBP would be affected by the formation of the 4:2 complex yet. This is the first structural basis of the inhibition mechanism where Tk-TIP26 prevents TBP from binding to TATA-DNA in the absence of TFB (Fig. 6C).
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). In the presence of excess amounts of Tk-TIP26, the quaternary complex of TIP26/TFB/TBP/ TATA-DNA is formed, and finally, equilibrium between the ternary and the quaternary complex would be achieved (Fig. 6C).
Conclusions
The structural studies on Tk-TIP26 allowed us to build a putative model of the Tk-TIP26/TBP complex, providing insights in the molecular mechanisms of the interaction between TIP26 and TBP. These insights will give us a clue for the understanding of the interaction between TBP and other TBP-interacting proteins. Crystallographic studies on the Tk-TIP26/Tk-TBP complex and the Tk-TIP26/Tk-TBP/Tk-TFB/TATA-DNA quaternary complex are in progress to increase our understanding of the transcription regulation mechanism by TIP26.
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Materials and methods |
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TOPAbstractIntroductionResults and DiscussionMaterials and methodsReferences |
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The initial phases were estimated by the MAD method using the SeMet data. Two of the three selenium sites in an asymmetric unit were found using Bijvoet difference Patterson methods. These heavy atom parameters were refined, and phase calculation and density modification were processed using the program CNS (Brünger et al. 1998). The quality of the corresponding electron density map was excellent. An initial model was built using the program O (Jones et al. 1994) and TURBO-FRODO (Jones 1985). Diffraction data of SeMet remote wavelength between 40 and 2.8 Å resolution were included in simulated annealing refinement with bulk solvent correction using CNS (Brünger et al. 1998). Ten percent of the reflections were kept separate to monitor Rfree, and were not used in the refinement. When an R-factor reached ~28%, the protein model was used to refine the native data up to 2.3 Å . After several rounds of manual rebuilding and refinement, the individual B factors were refined, along with the addition of solvent molecules. A zinc ion was placed on the site with ~5 
peak in an omit map. Zinc is the most probable metal because it shows a tetrahedral coordination geometry, and the temperature factor of the zinc ion modeled at the site had been refined to a value similar to those of the ligand atoms. The final refinement statistics are shown in Table 1. The current model contains regions of residues (–8–218) for a molecule in the asymmetric unit. No electron densities for the first 14 residues of the histidine-tag or C-terminal six residues were defined. These residues were eliminated from the refinement. Secondary structures were assigned with DSSP (Kabsch and Sander 1983).
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Preparation of Tk-TIP26/Tk-TBP complex and SDS-PAGE analysis
In order to prepare the Tk-TIP26/Tk-TBP complex, equal volumes of purified Tk-TIP26 (0.6 mM) and Tk-TBP (0.3 mM) were mixed and incubated at 303 K for 30 min. The mixed solution was applied to the gel filtration column Super-dex 200 10/30 HR column (GE Healthcare), equilibrated with 50 mM Tris-HCl (pH 6.8), 150 mM NaCl, and 1 mM DTT. The active fractions (shown in Fig. 4A) were pooled, and used in the SDS-PAGE analysis. The stoichiometry between Tk-TIP26 and Tk-TBP was estimated by SDS-PAGE analysis under the following conditions: Several concentrations of purified Tk-TIP26 (8.81, 3.26, 2.29, and 2.21 µM), Tk-TBP (7.70, 3.01, 2.57, and 1.92 µM), and purified Tk-TIP26/Tk-TBP complex were applied to 12.5% polyacrylamide gel, PAGEL (ATTO), and proceeded to SDS-PAGE analysis at 20 mA constant current. The resultant gel was stained with Coomassie brilliant blue (CBB) and intensities of the bands in the gel were estimated by the program Lane & Spot Analyzer (ATTO). Using these intensities, the calibration curves of Tk-TIP26 and Tk-TBP were prepared, and these curves were used to estimate the concentrations of Tk-TIP26 and Tk-TBP in the complex.
Preparation of figures
Figures 1A, 2A and B, 3, 4A and B, and 6A and B were prepared with the programs MOLSCRIPT (Kraulis 1991), RASTER3D (Merritt and Murphy 1994), and GRASP (Nicholls et al. 1993). Figure 1B was prepared with ALSCRIPT (Barton 1993); Figure 2C, with TopDraw (Collaborative Computing Project, Number 4 1994; Bond 2003).
Protein Data Bank accession code
Refined coordinates and structure factor have been deposited in the RCSB Protein Data Bank under the accession code 2CZR.
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4 Laboratory of Environmental Molecular Biology, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan.
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References |
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