Seth Darst and coworkers reported the high-resolution crystal structure for the core RNA polymerase from the bacteria T aquaticus (Taq). The protein has a total of five subunits that are present in the stoichiometry α2 ββ'ω. Each subunit is homologous with its E. coli counterpart. The ω subunit, which is not always present in isolated E. coli core RNA polymerase, may help to assemble the core RNA polymerase but is not required for RNA synthesis. The structural design of the Taq core RNA polymerase, along with the organization of its subunits.

    As evident from the orientation presented, the core polymerase resembles a crab claw. One pincer is almost entirely β subunit and the other almost entirely β' subunit. An internal groove or channel with many internal structural features runs along the full length of the core polymerase between the pincers. The channel is sufficiently wide to allow double-stranded DNA to fit inside. The core RNA polymerase is about 15 nm long (from the tips of the claws to the back) and 11 nm wide.

    Other noteworthy features of the Taq core RNA polymerase include the following:

1. The N-terminal domain (NTD) of one α subunit forms significant contacts with the corresponding domain in the other α subunit allowing the two α subunits to form a dimer. The two NTDs also bind the β-and β'-subunits. However the arrangement is not symmetrical because the NTD of one α subunit, α1 binds the β subunit while the NTD of the other α subunit, α2 binds the β' subunit. No residue in either α subunit has access to the channel of the core RNA polymerase where catalysis occure.

2. The β-and β'-subunits binds , which account for about 60% of the core RNA polymerases mass, interact extensively with each other. The catalytic site is formed by one such interaction at the base of the channel. The β' subunit provides an absolutely conserved-NADFDGD-motif that is essential for catalysis. The three aspartates in this motif, along with the magnesium ion that is bound to them, are required for phosphodiester bond formation. A second magnesium ion required at the active site is probably carried to this site by the incoming NTP.

3. The β' subunit forms a loop that extends into a main channel to form a rudder-like structure, which appears to be at the upstream edge of the transcription bubble, suggesting a possible role in separating RNA from the DNA-RNA hybrid.

4. The β' subunit has an absolutely conserved zinc binding motif containing four cysteine residues that is located outside the active site channel. Darst and coworkers propose that this region plays a structural rather than a catalytic role.