- Email: [email protected]
A second response in correcting the HslV–HslU quaternary structure
Journal of
Structural Biology Journal of Structural Biology 141 (2003) 7–8 www.elsevier.com/locate/yjsbi
Letter to the editor
A second response in correcting the HslV–HslU quaternary structure To the Editor: The first HslU–HslV structure, determined from cocrystals grown in the presence of AMP–PNP, has an unusual quaternary interface made of disordered loops (Bochtler et al., 2000). It raised numerous responses regarding its biological relevance and correctness. Overwhelming biochemical and structural data show that there is a single, but different, mode of HslU– HslV complex formation (Rohrwild et al., 1997; Sousa et al., 2000; Wang et al., 2001a,b; Ishikawa et al., 2000; Seong et al., 2002). To support their structure, the authors further showed that their co-crystals were enzymatically active in proteolysis, and consistent with new mutational data (Song et al., 2000). Because the original X-ray data were not available for verification of their structural analysis, I examined internal inconsistencies within the refined coordinates and suggested the coexistence of an alternative, biologically relevant complex in their co-crystals (Wang, 2001). In their response (Bochtler et al., 2001), the authors applied the molecular replacement calculations to a new structure of a second co-crystal grown in the presence of MgATP and the protein substrate resorufin–casein, without addressing the crystallographic issues on the first structure. In my previous response (Wang, 2001), I presented the evidence for the coexistence of the two modes of the HslU–HslV complex as a twinning problem in their crystals, which could account for their biochemical observations (Song et al., 2000), using the calculated structure factors from the refined coordinates for the approximation of the unavailable observed data (Bochtler et al., 2000). Twinning occurs frequently in the HslU and HslU–HslV systems (Wang et al., 2001a; Trame and McKay, 2001); when it does, the twinning fractions often vary from one crystal to another. In their response (Bochtler et al., 2001), the authors applied the so-called ‘‘Patterson cross-vector’’ calculations to a new structure of a second co-crystal that was grown in the presence of MgATP and the protein substrate resorufin– casein. These calculations did not address the twinning problem of the first co-crystals; in fact, the second crystal also has the twinning problem (Wang, 2001). These calculations were actually a variation of the molecular replacement method, because they were carried
out using the observed amplitudes (not intensities!) with phases derived from a partial model. Finally, I would like to point out that in their rebuttal, the authors have misquoted my previous response and misrepresented me on certain points (Bochtler et al., 2001; Wang, 2001). I did not suggest the Rtpart method as a general method. The authors have also misused the Rtpart method—they allowed model overlapping to occur during the Rtpart calculations, which would severely alter the amplitude distribution of structure factors. I did not state that there are ‘‘systematic’’ 70% differences in Wilson ratios between the calculated and observed data. I never suggested that there was, or there was not, a balance between ‘‘physiological HslU–HslV interactions and crystal packing forces’’ in their crystals. I also noted that in a more recent publication (Ramachandran et al., 2002), they suggested that their unusual mode of the complex formation could be due to an artifact of strong lattice forces, which appears inconsistent with their own previous biochemical data (Song et al., 2000). References Bochtler, M., Hartmann, C., Song, H.K., Bourenkov, G.P., Bartunik, H.D., Huber, R., 2000. The structures of HslU and the ATPdependent protease HslU-HslV. Nature 403, 800–805. Bochtler, M., Song, H.K., Hartman, C., Ramachandran, R., Huber, R., 2001. The quaternary arrangement of HslU and HslV in a cocrystal: a response to Wang, Yale. J. Struct. Biol. 135, 281–293. Ishikawa, T., Maurizi, M.R., Belnap, D., Steven, A.C., 2000. Docking of components of a bacterial complex. Nature 408, 667–668. Ramachandran, R., Hartmann, C., Song, H.K., Huber, R., Bochtler, M., 2002. Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY). Proc. Natl. Acad. Sci. USA 99, 7391–7401. Rohrwild, M., Pfeifer, G., Santarius, U., Muller, S.A., Huang, H.C., Engel, A., Baumeister, W., Goldberg, A.L., 1997. The ATPdependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome. Nat. Struct. Biol. 4, 133–139. Seong, I.S., Kang, M.S., Choi, M.K., Lee, J.W., Koh, O.J., Wang, J., Eom, S.H., Chung, C.H., 2002. The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase. J. Biol. Chem. 277, 25976–25982. Song, H.K., Hartman, C., Ramachandran, R., Bochtler, M., Behrendt, R., Moroder, L., Huber, R., 2000. Mutational studies on HslU and its docking model with HslV. Proc. Natl. Acad. Sci. USA 97, 14103–14108. Sousa, M.C., Trame, C.B., Tsuruta, H., Wilbanks, S.M., Reddy, V.S., McKay, D.B., 2000. Crystal and solution structures of an HslUV protease-chaperone complex. Cell 103, 633–643.
1047-8477/03/$ - see front matter Ó 2003 Elsevier Science (USA). All rights reserved. doi:10.1016/S1047-8477(02)00629-9
8
Letter to the editor / Journal of Structural Biology 141 (2003) 7–8
Trame, C.B., McKay, D.B., 2001. Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning. Acta Crystallogr. Sect. D 57, 1079–1090. Wang, J., 2001. A corrected quaternary arrangement of the peptidase HslV and ATPase HslU in a cocrystal structure. J. Struct. Biol. 134, 15–24. Wang, J., Song, J.J., Franklin, M.C., Kamtekar, S., Im, Y.J., Rho, S.H., Seong, I.S., Lee, C.S., Chung, C.H., Eom, S.H., 2001a. Crystal structures of the HslVU peptidase–ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure 9, 177–184.
Wang, J., Song, J.J., Seong, I.S., Franklin, M.C., Kamteker, S., Eom, S.H., Chung, C.H., 2001b. Nucleotide-dependent conformational changes in a protease-associated ATPase HslU. Structure 9, 1107– 1116.
Jimin Wang Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA E-mail address: [email protected]
Structural Biology Journal of Structural Biology 141 (2003) 7–8 www.elsevier.com/locate/yjsbi
Letter to the editor
A second response in correcting the HslV–HslU quaternary structure To the Editor: The first HslU–HslV structure, determined from cocrystals grown in the presence of AMP–PNP, has an unusual quaternary interface made of disordered loops (Bochtler et al., 2000). It raised numerous responses regarding its biological relevance and correctness. Overwhelming biochemical and structural data show that there is a single, but different, mode of HslU– HslV complex formation (Rohrwild et al., 1997; Sousa et al., 2000; Wang et al., 2001a,b; Ishikawa et al., 2000; Seong et al., 2002). To support their structure, the authors further showed that their co-crystals were enzymatically active in proteolysis, and consistent with new mutational data (Song et al., 2000). Because the original X-ray data were not available for verification of their structural analysis, I examined internal inconsistencies within the refined coordinates and suggested the coexistence of an alternative, biologically relevant complex in their co-crystals (Wang, 2001). In their response (Bochtler et al., 2001), the authors applied the molecular replacement calculations to a new structure of a second co-crystal grown in the presence of MgATP and the protein substrate resorufin–casein, without addressing the crystallographic issues on the first structure. In my previous response (Wang, 2001), I presented the evidence for the coexistence of the two modes of the HslU–HslV complex as a twinning problem in their crystals, which could account for their biochemical observations (Song et al., 2000), using the calculated structure factors from the refined coordinates for the approximation of the unavailable observed data (Bochtler et al., 2000). Twinning occurs frequently in the HslU and HslU–HslV systems (Wang et al., 2001a; Trame and McKay, 2001); when it does, the twinning fractions often vary from one crystal to another. In their response (Bochtler et al., 2001), the authors applied the so-called ‘‘Patterson cross-vector’’ calculations to a new structure of a second co-crystal that was grown in the presence of MgATP and the protein substrate resorufin– casein. These calculations did not address the twinning problem of the first co-crystals; in fact, the second crystal also has the twinning problem (Wang, 2001). These calculations were actually a variation of the molecular replacement method, because they were carried
out using the observed amplitudes (not intensities!) with phases derived from a partial model. Finally, I would like to point out that in their rebuttal, the authors have misquoted my previous response and misrepresented me on certain points (Bochtler et al., 2001; Wang, 2001). I did not suggest the Rtpart method as a general method. The authors have also misused the Rtpart method—they allowed model overlapping to occur during the Rtpart calculations, which would severely alter the amplitude distribution of structure factors. I did not state that there are ‘‘systematic’’ 70% differences in Wilson ratios between the calculated and observed data. I never suggested that there was, or there was not, a balance between ‘‘physiological HslU–HslV interactions and crystal packing forces’’ in their crystals. I also noted that in a more recent publication (Ramachandran et al., 2002), they suggested that their unusual mode of the complex formation could be due to an artifact of strong lattice forces, which appears inconsistent with their own previous biochemical data (Song et al., 2000). References Bochtler, M., Hartmann, C., Song, H.K., Bourenkov, G.P., Bartunik, H.D., Huber, R., 2000. The structures of HslU and the ATPdependent protease HslU-HslV. Nature 403, 800–805. Bochtler, M., Song, H.K., Hartman, C., Ramachandran, R., Huber, R., 2001. The quaternary arrangement of HslU and HslV in a cocrystal: a response to Wang, Yale. J. Struct. Biol. 135, 281–293. Ishikawa, T., Maurizi, M.R., Belnap, D., Steven, A.C., 2000. Docking of components of a bacterial complex. Nature 408, 667–668. Ramachandran, R., Hartmann, C., Song, H.K., Huber, R., Bochtler, M., 2002. Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY). Proc. Natl. Acad. Sci. USA 99, 7391–7401. Rohrwild, M., Pfeifer, G., Santarius, U., Muller, S.A., Huang, H.C., Engel, A., Baumeister, W., Goldberg, A.L., 1997. The ATPdependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome. Nat. Struct. Biol. 4, 133–139. Seong, I.S., Kang, M.S., Choi, M.K., Lee, J.W., Koh, O.J., Wang, J., Eom, S.H., Chung, C.H., 2002. The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase. J. Biol. Chem. 277, 25976–25982. Song, H.K., Hartman, C., Ramachandran, R., Bochtler, M., Behrendt, R., Moroder, L., Huber, R., 2000. Mutational studies on HslU and its docking model with HslV. Proc. Natl. Acad. Sci. USA 97, 14103–14108. Sousa, M.C., Trame, C.B., Tsuruta, H., Wilbanks, S.M., Reddy, V.S., McKay, D.B., 2000. Crystal and solution structures of an HslUV protease-chaperone complex. Cell 103, 633–643.
1047-8477/03/$ - see front matter Ó 2003 Elsevier Science (USA). All rights reserved. doi:10.1016/S1047-8477(02)00629-9
8
Letter to the editor / Journal of Structural Biology 141 (2003) 7–8
Trame, C.B., McKay, D.B., 2001. Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning. Acta Crystallogr. Sect. D 57, 1079–1090. Wang, J., 2001. A corrected quaternary arrangement of the peptidase HslV and ATPase HslU in a cocrystal structure. J. Struct. Biol. 134, 15–24. Wang, J., Song, J.J., Franklin, M.C., Kamtekar, S., Im, Y.J., Rho, S.H., Seong, I.S., Lee, C.S., Chung, C.H., Eom, S.H., 2001a. Crystal structures of the HslVU peptidase–ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure 9, 177–184.
Wang, J., Song, J.J., Seong, I.S., Franklin, M.C., Kamteker, S., Eom, S.H., Chung, C.H., 2001b. Nucleotide-dependent conformational changes in a protease-associated ATPase HslU. Structure 9, 1107– 1116.
Jimin Wang Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA E-mail address: [email protected]