Solution Structure of the Activator Contact Domain of the RNA Polymerase α Subunit

Abstract

The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase alpha subunit (alpha CTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface.

Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors

“…The best-characterized target on the RNA polymerase involved in molecular communication with transcription factors is the ␣ subunit carboxy-terminal domain (CTD) that contains the contact sites for class I transcription factors. The ␣ subunit, consisting of 329 amino acid residues, is composed of two structural domains, each responsible for distinct functions (1)(2)(3) and each forming independent structural domains connected by a protease-sensitive flexible linker (4)(5)(6). The amino (N)-terminal domain from residues 20 to 235 plays a key role in RNA polymerase assembly by providing the contact surface for ␣ dimerization and binding of ␤ and ␤Ј subunits (7)(8)(9)(10), whereas the CTD from residues 235 to 329 plays a regulatory role by providing the contact surfaces for trans-acting protein factors and cis-acting DNA elements (11)(12)(13)(14).…”

A nested set of C‐terminal deletions of the α subunit of Escherichia coli RNA polymerase define regions concerned with assembly, proteolysis, stabilization and transcriptional activation in vivo

“…The recent determination of the NMR structure of the C-terminal region of a confirms that it is an independently folded domain, separated from the N-terminal region by an unstructured loop (Jeon et al 1995). Moreover, the isolated C-terminal domain exhibits sequence-specific DNA binding activity and seems to contain an additional dimerization region (Blatter et al 1994).…”

“…On the two solution structures of the a C-terminal domain (Gaal et al 1996;Jeon et al 1995), this residue lies at the C-terminal end of the 'activator' helix H1(a 1 ) (see below). Clearly, the extreme C-terminal 13 residues play a key role, either indirectly by promoting the a C-terminal domain to fold in the appropriate conformation, thereby C-terminal truncated a derivatives The assembly levels of particular a deletions.…”

“…Finally, it is useful to summarize these in vivo results in the light of the two very recent NMR solution structures of the C-terminal domain (Jeon et al 1995;Gaal et al 1996). On these solution structures, the domain contains four helices (H1-H4 or a 1 -a 4 ) (Jeon et al 1995;Gaal et al 1996).…”

DNA Binding Specificity of Mu Transcription Factor C and Crystallization of C : DNA Complex

“…The α-CTD (8 kDa) plays a regulatory role by providing the contact surfaces for trans-acting regulatory protein factors and cis-acting DNA elements Gaal et al, 1996;Murakami et al, 1996). The α CTD binds the DNA minor groove upstream of the -35 hexamer using a helix-hairpin-helix (HhH) DNA binding motif (Jeon et al, 1995;Gaal et al, 1996;Shao and Grishin, 2000;Ross et al, 2001); this motif is called the 265 determinant (Gaal et al, 1996;Murakami et al, 1996). The α-CTD interacts with various transcription factors using the 287 determinant, which is made up of eight different amino-acid residues.…”