The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].

1: Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Jeon YH, Negishi T, Shirakawa M, Yamazaki T, Fujita N, Ishihama A, Kyogoku Y; Science 1995;270:1495-1497. PMID:7491496

2: The Escherichia coli RNA polymerase alpha subunit: structure and function. Ebright RH, Busby S; Curr Opin Genet Dev 1995;5:197-203. PMID:7613089

3: The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A; Proc Natl Acad Sci USA 1997;94:1709-1714. PMID:9050843