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Unformatted text preview: If you delete parts of the t rigger loop, reduce enzymatic action by 1000 fold. The green one is pulled away from the catatlytic site, then it folds in and closes on the catalytic site. Fork loop 2 has 3 different conformation. Can be an NTP binding site. From T. thermophilius, open conformation. Streptolydigin is the red component that inhibits transcription. Binds between fork loop 2, t rigger loop and bridge helix, locks polymerase open so it can’t make its conformational changes. One idea is that the t rigger loop has to open and close for every round of synthesis. If you lock it open and close it, significantly inhibit synthesis. Slide 36: View of the forkloop. Two different structures overlayed. Fork loop 2 in two different conformations (blue and yellow). In one, the DNA is frayed and open and interacting with fork loop 2. Suggested that it is significant in opening up downstream DNA. Two conformations from T. Thermophilus. Open one is Green: trapped by streptolidigin. Space filling view: looking down into secondary channel (where GreA and GreB bind, where various antibiotics bind, etc.). When t rigger loops is open, direct access into catalytic site. When it is closed, everything is completely closed down. Catalytic site in RNA pol is buried pretty deep inside. Open conformation: only 12 angstroms wide, 45 angstroms deep. Catalytic site is buried, striking since the enzyme has to sample all 4 NTPs. Does not know what is the right NTP until it is already bound. Big conundrums about NTPs—is there a trafficking problem? Must shuttle all NTPs in and out. Movie: starts where substrate binds. Trigger loop closes (undergoes conformational change). Bond formation, trigger loop opens. Translocates Base moves across top of bride helix, bridge helix moves. Twist base into catalytic site (two step process)....
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This note was uploaded on 03/03/2010 for the course CHEM 431 taught by Professor Pielak during the Spring '07 term at UNC.
- Spring '07