Question

In the elongation complex of RNA polymerase II, what is the role of the clamp? the zipper? the lid? the rudder?

Answer 1

As per the RNA POLYMERASE II structure, it is divided into four modules, including a "clamp". The swinging motion of the clamp, produces a greater opening of the cleft in form 2 than form 1 which may permit the entry of promoter DNA for the initiation of transcription. In a transcribing complex, the clamp behaves like a multifunctional element. The unique clamp fold, is formed by N- and C- terminal regions of Rbp1 and C-terminal region of Rpb2. This is stabilized by three zinc ions, two within the "clamp core" and one underlying at the upper end, termed the "clamp head". At , its base the clamp region is connected to the cleft region of Rbp1, to the "anchor" region of Rbp2 and to Rbp6, through a set of "switch" regions that are flexible and enable clamp movement.

The "lid" and "zipper" maintain the upstream end of transcription bubble.

The"'rudder" and "lid" are involved in seperation of DNA -RNA.