Abstract
Multi-subunit RNA polymerases of the two double-Ψ–β-barrel type are among the most beautiful, complex, and dynamic proteins in the human biosphere. Furthermore, multi-subunit RNA polymerases, their general transcription factors, and promoters form the core of the narrative of evolution of life on earth. In this chapter, I use a bacterial RNA polymerase–initiating complex (PDB 4XLN) interacting with promoter DNA to describe some of the features of these essential enzymes. So, this chapter is an attempt to look under the hood and partly disassemble the perplexing RNA polymerase motor. The RNA polymerase structure I selected is from Thermus thermophilus, a bacterial hyperthermophile. A bacterial RNA polymerase was selected because it is slightly simpler than archaeal and eukaryotic RNA polymerases in subunit structure and has fewer zinc (Zn) atoms. Otherwise, because of evolution, features of bacterial RNA polymerase are also features of archaeal and eukaryotic RNA polymerases.
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