T7 RNA Polymerase: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
Jaime Prilusky (talk | contribs)
ConfirmAccount, Editor, Mutation, Next, Print3D, Tester, any2jmol, Bureaucrats, Interface administrators, journal, print3d, Administrators, tester
8,782 edits
No edit summary
 
(3 intermediate revisions by 2 users not shown)
Line 16: Line 16:
'''The initial bubble grows'''. From 2mer, the system progresses ->3mer->4mer->5mer->6mer ...  During this time, the newly formed RNA-DNA duplex (hybrid) grows, from 2 bases, to <scene name='77/778917/T7rp_3mer_rna_backedout/1'>3 bases</scene>, to 4 bases, to 5 bases, to 6 bases, to<scene name='77/778917/T7rp_7mer_rna_backedout/1'> 7 bases</scene>, to <scene name='77/778917/T7rp_8mer_rna_backedout/1'>8 bases</scene>, etc., and during the time, the duplex is short and otherwise unstable.  
'''The initial bubble grows'''. From 2mer, the system progresses ->3mer->4mer->5mer->6mer ...  During this time, the newly formed RNA-DNA duplex (hybrid) grows, from 2 bases, to <scene name='77/778917/T7rp_3mer_rna_backedout/1'>3 bases</scene>, to 4 bases, to 5 bases, to 6 bases, to<scene name='77/778917/T7rp_7mer_rna_backedout/1'> 7 bases</scene>, to <scene name='77/778917/T7rp_8mer_rna_backedout/1'>8 bases</scene>, etc., and during the time, the duplex is short and otherwise unstable.  


'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 basepair RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 nucleotides of RNA synthesized. In the morph shown <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_timing_t7rnap.pdb|Coordinates] available on Proteopedia</ref>, models of how the structure might look with 4, 5, and 6 nucleotides of RNA synthesized were interpolated from the existing structures with 3 and 7 nucleotides of RNA.  
'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 basepair RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 nucleotides of RNA synthesized. In the morph shown <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_timing_t7rnap.pdb Coordinates] available on Proteopedia</ref>, models of how the structure might look with 4, 5, and 6 nucleotides of RNA synthesized were interpolated from the existing structures with 3 and 7 nucleotides of RNA. In this <jmol>
  <jmolLink>
    <script> anim off; delay 0.5; model 0; display 1.1; delay 0.5;
display 1.2 or 1.1 and (RNA or 14); delay 0.5
display 1.3 or 1.1 and (RNA or 14-15); delay 0.5
display 1.4 or 1.1 and (RNA or 14-16); delay 0.5
display 1.5 or 1.1 and (RNA or 14-16) or 1.2 and RNA; delay 1.5;display all;model 1;
</script>
    <text>alternate sequence</text>
  </jmolLink>
</jmol>, the growing hybrid is shown explicitly (with some modeling problem for 6 nucleotides if you look closely).


'''Transition to Elongation'''. Toward the end of the above rotation (at about a 9mer RNA), stress builds up in the promoter binding domain, leading to a weakening of some of the interactions with the upstream duplex promoter. This triggers promoter release, which now allows the N-terminal domain to rotate 220° in the ''other'' direction, to form the <scene name='77/778917/T7rp_elongation_cmplx_full_vw/1'>elongation complex</scene>.
'''Transition to Elongation'''. Toward the end of the above rotation (at about a 9mer RNA), stress builds up in the promoter binding domain, leading to a weakening of some of the interactions with the upstream duplex promoter. This triggers promoter release, which now allows the N-terminal domain to rotate 220° in the ''other'' direction, to form the <scene name='77/778917/T7rp_elongation_cmplx_full_vw/1'>elongation complex</scene>.
Line 31: Line 41:


</StructureSection>
</StructureSection>
== Files for 3D printer ==
<i class="fas fa-cubes"></i> T7 RNA polymerase model by [[User:Marius Mihasan|Marius Mihasan]] [https://3dprint.nih.gov/discover/3dpx-015377  <i class="fas fa-download"></i>]
== References ==
== References ==
1,"1aro","Free enz plus lysozyme","T7RP with the bound inhibitor T7 lysozyme, no DNA - Jeruzalmi, D. & Steitz, T. A. (1998) EMBO J 17, 4101-4113"
1,"1aro","Free enz plus lysozyme","T7RP with the bound inhibitor T7 lysozyme, no DNA - Jeruzalmi, D. & Steitz, T. A. (1998) EMBO J 17, 4101-4113"
Line 59: Line 72:


<references/>
<references/>
[[Category:3D printer files]]
Retrieved from "https://proteopedia.org/T7_RNA_Polymerase"