View source for Journal:Science:1

<StructureSection load='' size='450' side='right' scene='73/733981/Cv/22' caption=''>
===  Structural basis of transcription activation ===
<big>Yu Feng, Yu Zhang, Richard H. Ebright</big> <ref>PMID: 27284196</ref>
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<b>Molecular Tour</b><br>
Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)–promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises ''Thermus thermophilus'' transcription activator protein TTHB099 (TAP) [homolog of ''Escherichia coli'' catabolite activator protein (CAP)], ''T. thermophilus'' RNAP σ<sup>A</sup> holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.

<scene name='73/733981/Cv/31'>TAP, RNAP holoenzyme, DNA and RNA</scene>.

<scene name='73/733981/Cv/32'>DNA/RNA/protein interactions</scene>.

To obtain a structure of TAP-RPo, we used a <scene name='73/733981/Cv/12'>nucleic-acid scaffold corresponding to positions –57 to +15</scene> (-54 to +11 shown) of a class II TAP-dependent promoter (positions numbered relative to transcription start site). Pink, nontemplate strand; red, template strand. The scaffold contained a <scene name='73/733981/Cv/13'>consensus DNA site for TAP centered between positions –41 and –42</scene> (TAP site: cyan, template strand; deeppink, nontemplate strand), a near-consensus <scene name='73/733981/Cv/23'>extended –10 element</scene> (violet), a <scene name='73/733981/Cv/15'>consensus –10 element</scene> (blue), a <scene name='73/733981/Cv/16'>consensus discriminator element</scene> (royalblue), a consensus core recognition element, a <scene name='73/733981/Cv/17'>13-bp transcription bubble</scene> (maintained in the unwound state by having noncomplementary sequences on nontemplate and template strands), and UpCpGpA (in magenta).

<scene name='73/733981/Cv1/12'>Comparison of TAP-DNA in TAP-RPo to CAP-DNA</scene>. TAP in cyan, CAP in skyblue. <scene name='73/733981/Cv1/13'>Click here to see animation of this scene</scene>.

'''Protein-DNA interactions'''

*<scene name='73/733981/Cv1/8'>TAP binding</scene>. TAP is in cyan/dodgerblue. Pink, nontemplate strand; red, template strand.
*<scene name='73/733981/Cv1/7'>TAP binding (90° rotation)</scene>.
*<scene name='73/733981/Cv1/14'>TAP site</scene>. TAP is in cyan, σ is in yellow. Pink, nontemplate strand; red, template strand. 
*<scene name='73/733981/Cv1/2'>Interactions between σR4 and –35 region</scene>.
*<scene name='73/733981/Cv1/3'>Interactions between σR3 and extended –10 element</scene> (in violet). 
*<scene name='73/733981/Cv1/4'>Interactions between σR2 consensus –10 element</scene> (in blue).
*<scene name='73/733981/Cv1/5'>Protein-DNA interactions that mediate promoter recognition</scene>.
*<scene name='73/733981/Cv1/9'>σ conserved region σR1.2 interacts with nontemplate-strand ssDNA of the discriminator element</scene> (in royalblue).
*<scene name='73/733981/Cv/34'>DNA/RNA/protein interactions after the discriminator element</scene>.


  
</StructureSection>

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