The X-ray crystal structure of RNA polymerase from Archaea

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  • An Erratum to this article was published on 13 March 2008


The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB1,2. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits3,4. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 Å resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 Å) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron–sulphur (Fe–S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.

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Figure 1: Three-dimensional structure of the archaeal RNAP.
Figure 2: Cellular RNAP structures from three domains of life.
Figure 3: Structures around the foot domains from three domains of life.
Figure 4: The Fe–S cluster may play a structural role in D-subunit folding.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors have been deposited at the Protein Data Bank (accession codes 2PMZ and 2PA8 for the S. solfataricus RNAP and D/L subcomplex structures, respectively).


  1. 1

    Bell, S. D. & Jackson, S. P. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6, 222–228 (1998)

  2. 2

    Geiduschek, E. P. & Ouhammouch, M. Archaeal transcription and its regulators. Mol. Microbiol. 56, 1397–1407 (2005)

  3. 3

    Todone, F., Brick, P., Werner, F., Weinzierl, R. O. & Onesti, S. Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol. Cell 8, 1137–1143 (2001)

  4. 4

    Yee, A. et al. Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum . Proc. Natl Acad. Sci. USA 97, 6311–6315 (2000)

  5. 5

    Ebright, R. H. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304, 687–698 (2000)

  6. 6

    Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811–824 (1999)

  7. 7

    Murakami, K. S., Masuda, S. & Darst, S. A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296, 1280–1284 (2002)

  8. 8

    Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863–1876 (2001)

  9. 9

    Bushnell, D. A., Westover, K. D., Davis, R. E. & Kornberg, R. D. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms. Science 303, 983–988 (2004)

  10. 10

    Wang, D., Bushnell, D. A., Westover, K. D., Kaplan, C. D. & Kornberg, R. D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941–954 (2006)

  11. 11

    Bushnell, D. A. & Kornberg, R. D. Complete, 12-subunit RNA polymerase II at 4.1-Å resolution: implications for the initiation of transcription. Proc. Natl Acad. Sci. USA 100, 6969–6973 (2003)

  12. 12

    Armache, K. J., Kettenberger, H. & Cramer, P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl Acad. Sci. USA 100, 6964–6968 (2003)

  13. 13

    Armache, K. J., Mitterweger, S., Meinhart, A. & Cramer, P. Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J. Biol. Chem. 280, 7131–7134 (2005)

  14. 14

    Westover, K. D., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119, 481–489 (2004)

  15. 15

    Goede, B., Naji, S., von Kampen, O., Ilg, K. & Thomm, M. Protein–protein interactions in the archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J. Biol. Chem. 281, 30581–30592 (2006)

  16. 16

    Fernandez-Tornero, C. et al. Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III. Mol. Cell 25, 813–823 (2007)

  17. 17

    Ouhammouch, M., Werner, F., Weinzierl, R. O. & Geiduschek, E. P. A fully recombinant system for activator-dependent archaeal transcription. J. Biol. Chem. 279, 51719–51721 (2004)

  18. 18

    Naji, S., Grunberg, S. & Thomm, M. The RPB7 orthologue E′ is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J. Biol. Chem. 282, 11047–11057 (2007)

  19. 19

    Werner, F. & Weinzierl, R. O. Direct modulation of RNA polymerase core functions by basal transcription factors. Mol. Cell. Biol. 25, 8344–8355 (2005)

  20. 20

    Chlenov, M. et al. Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta′ subunit. J. Mol. Biol. 353, 138–154 (2005)

  21. 21

    Ishihama, A., Taketo, M., Saitoh, T. & Fukuda, R. in RNA polymerase (eds Losick, R. & Chamberlin, M.) 485–502 (Cold Spring Harbor Laboratory, New York, 1976)

  22. 22

    Zillig, W., Palm, P. & Heil, A. in RNA polymerase (eds Losick, R. & Chamberlin, M.) 101–125 (Cold Spring Harbor Laboratory, New York, 1976)

  23. 23

    Rodriguez-Monge, L., Ouzounis, C. A. & Kyrpides, N. C. A ferredoxin-like domain in RNA polymerase 30/40-kDa subunits. Trends Biochem. Sci. 23, 169–170 (1998)

  24. 24

    Thomas, M. C. & Chiang, C. M. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol. 41, 105–178 (2006)

  25. 25

    Zalenskaya, K. et al. Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products. Gene 89, 7–12 (1990)

  26. 26

    Murakami, K. et al. Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. Proc. Natl Acad. Sci. USA 94, 11274–11278 (1997)

  27. 27

    Kapanidis, A. N. et al. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144–1147 (2006)

  28. 28

    Vassylyev, D. G. et al. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 163–168 (2007)

  29. 29

    Werner, F. & Weinzierl, R. O. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol. Cell 10, 635–646 (2002)

  30. 30

    Campbell, E. A. et al. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104, 901–912 (2001)

  31. 31

    Otwinowski, Z. & Minor, W. in Macromolecular Crystallography Part A (ed. Charles W. Carter Jr) 307–326 (Academic Press, New York, 1997)

  32. 32

    McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D Biol. Crystallogr. 61, 458–464 (2005)

  33. 33

    Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965–972 (2000)

  34. 34

    Brunger, A. T. et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

  35. 35

    Winn, M. D., Isupov, M. N. & Murshudov, G. N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D 57, 122–133 (2001)

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We thank L. Berman and A. Héroux at the National Synchrotron Light Source, D. Lessner and H. Yennawar at The Pennsylvania State University, and D. Bushnell and R. Kornberg at Stanford University for help. We thank E. P. Geiduschek, J. G. Ferry, S. A. Darst, F. Asturias, V. Lamour and R. Yajima for critiques of the manuscript. This work was supported by The Pew Scholars Program in the Biomedical Sciences and supported in part by the National Institutes of Health.

Author Contributions A.H. crystallized and solved the structures of the S. solfataricus RNAP and D/L subcomplex. B.J.K. supported the RNAP purification and its structure determination. K.S.M. and A.H. wrote the manuscript, and all authors discussed the results and commented on the manuscript.

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Correspondence to Katsuhiko S. Murakami.

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The file contains Supplementary Discussion, Supplementary Tables 1-4, additional references and Supplementary Figures 1-16 with Legends. (PDF 5965 kb)

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Hirata, A., Klein, B. & Murakami, K. The X-ray crystal structure of RNA polymerase from Archaea. Nature 451, 851–854 (2008) doi:10.1038/nature06530

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