Jimin Wang
Director of Center for Structural Biology
X-ray intensity corrections for crystals containing lattice-translocation defects
Lattice translocation defects are caused by the random translocation of some layers by a fixed constant within the stacked layers of a crystal. When such events result in the fragmentation of the crystal into smaller mosaic blocks, the observed intensities are simply additive from each block and independent of the translocation vector. When such events occur within one single coherent mosaic block, interference in X-ray diffraction is observed with the intensities modulated by a factor that is a function of this translocation vector and the fractions of the translocated and un-translocated layers (Wang et al., 2005). This phenomenon was first observed nearly 50 years ago (Bragg and Howells 1954; Cochran and Howells 1954; Howells and Perutz 1954). The atomic structures of crystals containing the lattice-translocation defects were considered to be unsolvable (Glauser and Rossmann 1966; Pickersgill 1987). Recently, an equation for the modulation factor caused by these defects was formulated and the observed intensities become correctable using this factor (Wang et al., 2005).
Because of lattice translocation defects, two identical but translated lattices can co-exist as a single coherent mosaic block in a crystal. The observed structure in such cases is a weighted sum of two identical but translated structures, one from each lattice; the observed structure factors are a weighted vector sum of the structure factors with identical unit amplitudes but shifted phases. In this report, we correct X-ray intensities from a single crystal containing these defects of the hybrid HslV-HslU complex, which consists of E. coli HslU and B. subtilis HslV (also known as CodW). When intensities are not corrected, a biologically irrelevant complex (with CodW from one lattice and HslU from another) is implied to exist. Only upon correction does a biologically functional CodW-HslU complex structure emerge.
References
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Cochran, W., and Howells, E.R. (1954). X-ray diffraction by a layer structure containing random displacements. Acta Cryst. 7, 412-415.
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Howells, E.R., and Perutz, M.F. (1954). The structure of haemoglobin V. Imidazole-methaemoglobin: a further check of the signs. Proc. Roy. Soc. A225, 308-314.
Kamtekar, S., Berman, A., Wang, J., Lazaro, J.M., deVega, M., Blanco, L., Salas, M., and Steitz, T.A. (2004). The structural basis of strand displacement and processivity in the protein-primed DNA polymerase from bacteriophage f29. Molecular Cell 16, 609-618.
Pickersgill, R.W. (1987). One-dimensional disorder in spinach ribulose bisphosphate carboxylase crystals. Acta Cryst. A43, 502-506.
Wang, J., Kamtekar, S., Berman, A.J., Steitz, T.A. (2005) Correction of X-ray intensities from single crystals containing lattice-translocation defects. Acta Cryst. D61, 67-74.
Wang, J., Rho, S.H., Park, H.H., Eom, S.H. (2005) Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects. Acta Cryst. D (in press).
Recent cyanobacterial Kai protein structures suggest a rotary clock
The cyanobacterial circadian oscillator, which controls internal daily periodicity, consists of three Kai proteins, KaiA, KaiB, and KaiC, in its oscillation feedback loop (Ishiura et al., 1998). KaiC is a negative element of the loop, repressing the expression of its own KaiBC and other global genes; KaiA is a positive element, releasing the repression. The discovery of a bacterial clock unexpectedly breaks the paradigm of biological clocks, because rapid cell division and chromosome duplication in bacteria occur within one circadian period (Kondo et al., 1994, 1997). In fact, these cyanobacterial oscillators in individual cells have a strong temporal stability with a correlation time of several months (Mihalcescu et al., 2004). The cyanobacterial circadian system is the simplest of all clock forms and possesses the same three levels of organizations as do all other biological clocks: the generation of oscillation in its feedback loop, amplification of oscillating signals for gene expression, and coordination with daily environmental events (Harmer et al., 2001). Structural comparison reveals that the Kai system resembles the F1-ATPase system in which KaiC is equivalent to a3b3, KaiA to gde, and KaiB to its inhibitory factor. It also suggests that there exists a possible haemagglutinin-like spring-loaded mechanism for the activation of KaiA during formation of Kai complexes.
References
Wang, J. (2005). Recent cyanobacterial Kai protein structures suggest a rotary clock. Structure (May issue).
Pattanayek, R., Wang, J., Tetsuya, M., Xu., Johnson, C.H., Egli, M. (2004) . Visualizing a circadian clock protein: crystal structure of KaiC and functional insights. Mol. Cell 15, 375-388.
Harmer, S.L., Panda, S., and Kay, S.A. (2001). Molecular bases of circadian rhythms. Annu. Rev. Cell Dev. Biol. 17, 215-253.
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Kondo, T., Mori, T., Lebedeva, N.V., Aoki, S., Ishiura, M., Golden, S.S. (1997). Circadian rhythms in rapidly dividing cyanobacteria. Science 275, 224-227.
Mihalcescu, I., Hsing, W., Leibler, S. (2004). Resilient circadian oscillator revealed in individual cyanobacteria. Nature 430, 81-85.
Ishiura, M., Kutsuna, S., Aoki, S., Iwasaki, H., Andersson, C.R., Tanabe, A., Golden, S.S., Johnson, C.H., and Kondo, T. (1998). Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria. Science 281, 1519-1523.
Nucleotide-dependent domain motions within rings of the RecA/AAA+ superfamily
All Extended ATPase Associated cellular Activities or AAA+ proteins belong to the RecA superfamily because they include at lease one RecA fold nucleotide-binding domain or NBD (Story et al., 1992; Story and Steitz, 1992; Story et al., 1993; Neuwald et al., 1999; Leipe et al., 2000). This family includes the DNA bacterial conjugation protein TrwB, DNA helicases, the F1-ATPase, some protein-folding chaperone ATPases, peptidase-associated unfoldases, and ATP-dependent transcription regulators (Story et al., 1993; Neuwald et al., 1999; Leipe et al., 2000). Structurally, many members of this family are hexameric or rarely heptameric rings (Vale, 2000), and their conformations are controlled by their interactions with nucleotides. The functional diversity of these proteins derives from the auxiliary domains attached to their RecA-fold NBDs, which interact with different partners and propagate the mechanical forces that are generated by NBDs. For example, auxiliary domains interact with partner peptidases and protein substrates in the ATP-dependent protease family of AAA+ proteins (Wang et al., 1997; Wang et al., 1998; Wang et al., 2001a; Beuron et al., 1998; Hochstrasser and Wang, 2001), and they interact with s54-RNA polymerase and perhaps also with DNA substrates in the ATP-dependent transcription regulatory factor family of AAA+ proteins (Zhang et al., 2002; Elderkin et al., 2002).
The oligomeric rings formed by RecA-fold proteins are mechanochemical motors that perform many important biological functions. Their RecA-fold domains convert the chemical energy of ATP into mechanical work through large nucleotide-dependent conformational changes. The F1-ATPase ring for example generates the force perpendicular to the ring axis, while the HslU ring generates forces parallel to it. There exists a strong correlation between the directions of forces generated and the orientation of the RecA folds, not only in these two proteins but also in T7 DNA helicase, suggesting that it should be possible to predict the direction of forces generated by other members of this family on the basis of the orientation of their RecA folds.
References
Wang, J. (2004). Nucleotide-dependent domain motions with rings of the Re cA/AAA+ superfamily. J. Struct. Biol. 148, 259-267.
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., and Eom, S.H. (2001a). Crystal structures of the HslVU peptidase-ATPase complex suggest an ATP-dependent proteolysis mechanism. Structure 9, 177-184.
Wang, J., Song, J.J., Seong, I.S., Franklin, M.C., Kamtekar, S., Eom, S.H., and Chung, C.H. (2001b). Nucleotide-dependent conformational changes in a protease-associated ATPase HslU. Structure 9, 1107-1116.
Wang, J., and Boisvert, D.C., (2003). Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0Å resolution. J. Mol. Biol. 327, 843-855.
Wang, J., Hartling, J.A., and Flanagan, J.M., (1997). The structure of ClpP at 2.3Å resolution suggests a model for ATP-dependent proteolysis. Cell 91, 447-456.
Wang, J., Hartling, J.A., and Flanagan, J.M. (1998). Crystal structure determination of Escherichia coli ClpP starting from an EM-derived mask. J. Struct. Biol. 124, 151-163.
Hochstrasser, M., and Wang, J. (2001). Unraveling the means to the end in ATP-dependent proteases. Nature Struct. Biol. 8, 294-296.
Leipe, D.D., Aravind, L., Grishin, N.V., and Koonin, E.V. (2000). The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res. 10, 5-16.
Neuwald, A.F., Aravind, L., Spouge, J.L., and Koonin E.V. (1999). AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27-43.
Story, R.M., Bishop, D.K., Kleckner, N., and Steitz, T.A. (1993). Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science 259, 1892-1896.
Story, R.M., and Steitz, T.A. (1992). Structure of the RecA protein-ADP complex. Nature 355, 374-376.
Story, R.M., Weber, I.T., and Steitz, T.A. (1992). The structure of the E. coli RecA protein monomer and polymer. Nature 355, 318-325.
Vale, R.D. (2000). AAA proteins. Lords of ring. J. Cell. Biol. 150, F13-19.
Zhang, X. Shaw, A., Bates, P.A., Newman, R.H., Gowen, B., Orlova, E., Gorman, M.A., Kondo, H., Dokurno, P., Lally, J., Leonard, G., Meyer, H., van Heel, M., and Freemont, P.S. (2000). Structure of the AAA ATPase p97. Mol. Cell 6, 1473-1484.
Group I intron structure and RNA structural genomics
The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. Here we report the X-ray crystal structure (3.1-A resolution) of a complete group I bacterial intron in complex with both the 5’- and the 3’-exons. This complex corresponds to the splicing intermediate before the exon ligation step. It reveals how the intron uses structurally unprecedented RNA motifs to select the 5’- and 3’-splice sites. The 5’-exon’s 3’-OH is positioned for inline nucleophilic attack on the conformationally constrained scissile phosphate at the intron-3’-exon junction. Six phosphates from three disparate RNA strands converge to coordinate two metal ions that are asymmetrically positioned on opposing sides of the reactive phosphate. This structure represents the first splicing complex to include a complete intron, both exons and an organized active site occupied with metal ions.
A structure-designed crystallization lattice-design approach is underway which will allow to determine structures of any RNA of interest.
References
Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A. (2004) Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50.
Strobel, S.A., Adams, P.L., Stahley, M.R., Wang, J. (2004) RNA kink turns the left and the right. RNA 10, 1852-1854.
Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A. (2004) Crystal structure of a group I intro splicing intermediate. RNA 10, 1867-1887.