T7 RNA Polymerase

T7 RNA polymerase , by recognizing the upstream duplex region of the promoter (-17 to -5), and then melting a bubble (-4 to about +3), within the larger duplex. The duplex promoter domain binds primarily to the N-terminal domain of the enzyme, with the exception of the (C-terminal domain) "." It is the combination of the N-terminal domain, with the positioned specificity loop, that forms the specific binding surface.

Strong interactions with the duplex region of the promoter places the "intercalating loop" into the DNA between residues -4 and -5. The intercalating loop, also called the Valine Loop, has hydrophobic residues Val, Ile, etc that stack on and stabilize the exposed face of the base pair at position -5, stabilizing the locally melted structure.

Melting of a bubble within the DNA allows the (single stranded) template strand to enter the active site, and allows template strand bases +1 and +2 to orient in the active site, poised for initiation

. The enzyme then binds the first two substrate NTP's, as directed by the template (typically two GTP's, encoded by CC in the template strand). A phosphoryl transfer reaction occurs to form the product dinucleotide (pppGpG).

At this point, the complex is in the pre-translocated state and to add the next base, the enzyme must translocate forward along the DNA (or equivalently, the RNA/DNA slides backwards), forming the post-translocated state. In the latter state (only) the active site now accommodates binding of the next NTP to the (+3) template base.

Function

Disease

Relevance

Structural highlights

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.