Papers In Press, published online ahead of print April 21, 2006
J. Biol. Chem, 10.1074/jbc.M513241200
Submitted on December 13, 2005
Revised on April 19, 2006
Accepted on April 21, 2006
Structural, biochemical and dynamic characterizations of the hRPB8 subunit of human RNA polymerases
Xue Kang, Yunfei Hu, You Li, Xianrong Guo, Xiaolu Jiang, Luhua Lai, Bin Xia, and Changwen Jin
Beijing NMR Center, Peking University, Beijing, Beijing 100871
Corresponding Author: changwen{at}pku.edu.cn
The RPB8 subunit is present in all three types of eukaryotic RNA polymerases and is highly conserved during the evolution. It is an essential subunit required for the transcription of nuclear genes, but the detailed mechanism including its interactions with different subunits and oligonucleotides remains largely unclear. Herein, we report the three-dimensional structure of human RPB8 (hRPB8) at high resolution determined by NMR spectroscopy. The protein fold comprises an eight stranded bbarrel, six short helices and a large unstructured omega-loop. The overall structure of hRPB8 is similar to that of yRPB8 from Saccharomyces cerevisiae, and belongs to the oligonucleotide/oligosaccharide-binding fold. However, several features of the tertiary structures are notably different between the two proteins. In particular, hRPB8 has a more clustered positively charged binding interface with the largest subunit RPB1 of the RNA polymerases. We employed biochemical methods to detect its interactions with different single-stranded DNA sequences. In addition, single-stranded DNA titration experiments were performed to identify the residues involved in non-specific binding with different DNA sequences. Furthermore, we characterized the millisecond-timescale conformational flexibility of hRPB8 upon its binding to single-stranded DNA. The current results demonstrate that hRPB8 interacts with single-stranded DNA non-specifically and adopts significant conformational changes, and the hRPB8/single-stranded DNA complex is a fast exchanging system. The solution structure in conjunction with the biochemical and dynamic studies reveal new aspects of this subunit in the molecular assembly and the biological function of the human nuclear RNA polymerases.