Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum

Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum

^*Department of Biochemistry and Molecular Biology, Department of Chemistry, and The Biotechnology Laboratory, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; ^†Division of Molecular and Structural Biology, Ontario Cancer Institute, and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, Canada M5G 2M9; and ^‡Banting and Best Department of Medical Research, C. H. Best Institute, University of Toronto, Toronto, ON, Canada M5G 1L6

Edited by Roger D. Kornberg, Stanford University School of Medicine, Stanford, CA, and approved April 5, 2000 (received for review March 20, 2000)

Abstract

The RNA polymerase subunit RPB10 displays a high level of conservation across archaea and eukarya and is required for cell viability in yeast. Structure determination of this RNA polymerase subunit from Methanobacterium thermoautotrophicum reveals a topology, which we term a zinc-bundle, consisting of three α-helices stabilized by a zinc ion. The metal ion is bound within an atypical CX₂CX_nCC sequence motif and serves to bridge an N-terminal loop with helix 3. This represents an example of two adjacent zinc-binding Cys residues within an α-helix conformation. Conserved surface features of RPB10 include discrete regions of neutral, acidic, and basic residues, the latter being located around the zinc-binding site. One or more of these regions may contribute to the role of this subunit as a scaffold protein within the polymerase holoenzyme.

Footnotes

↵ § To whom reprint requests should be addressed at: Department of Biochemistry, 2146 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada V6T 1Z3. E-mail: mcintosh{at}otter.biochem.ubc.ca.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The coordinates and restraint tables have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID code 1EF4). The NMR chemical shifts have been deposited in the BioMagResBank, www.bmrb.wisc.edu (accession no. 4571).
Abbreviations:

RNAP,

RNA polymerase;

3D,

three-dimensional