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

Abstract

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).

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Acknowledgements

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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Supplementary Information

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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