T7 RNA Polymerase: Difference between revisions

Line 7:

'''Positioning of the +1 base in the active site'''. 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.

'''Catalysis'''. The enzyme then <scene name='77/778917/T7rp_gg_bound/1'>binds the first two substrate NTP's</scene>, 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).

'''Catalysis'''. The enzyme then <scene name='77/778917/T7rp_gg_bound/1'>binds the first two substrate NTP's</scene>, as directed by the template (typically two GTP's, encoded by CC in the template strand). The <scene name='77/778917/T7rp_gg_phosphoryl_xfer/1'>3' hydroxyl of the +1 NTP attacks the alpha phosphate of the +2 NTP</scene> to initiate a phosphoryl transfer reaction. Release of pyrophosphate (PPi) leaves the product dinucleotide (pppGpG) in the active site. Note that one of the <scene name='77/778917/T7rp_gg_phosphoryl_xfer/1'>Mg(II) ions stabilizes the leaving group beta-gamma pyrophosphate</scene> (diphosphate).

'''Movement'''. 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.

T7 RNA Polymerase: Difference between revisions

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@@ Line 7: / Line 7: @@
 '''Positioning of the +1 base in the active site'''. 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.
-'''Catalysis'''. The enzyme then <scene name='77/778917/T7rp_gg_bound/1'>binds the first two substrate NTP's</scene>, 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).
+'''Catalysis'''. The enzyme then <scene name='77/778917/T7rp_gg_bound/1'>binds the first two substrate NTP's</scene>, as directed by the template (typically two GTP's, encoded by CC in the template strand). The <scene name='77/778917/T7rp_gg_phosphoryl_xfer/1'>3' hydroxyl of the +1 NTP attacks the alpha phosphate of the +2 NTP</scene> to initiate a phosphoryl transfer reaction. Release of pyrophosphate (PPi) leaves the product dinucleotide (pppGpG) in the active site. Note that one of the <scene name='77/778917/T7rp_gg_phosphoryl_xfer/1'>Mg(II) ions stabilizes the leaving group beta-gamma pyrophosphate</scene> (diphosphate).
 '''Movement'''. 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.