View source for User:Jaime Prilusky/Test/Beta-Prime Subunit of Bacterial RNA Polymerase

==Bacterial RNA Polymerase: New Insights on a Fundamental Molecular Machine==
<StructureSection load='2o5j' size='400' side='right' caption='β’ Subunit of Bacterial RNAP' scene='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_overview_1/1'>
===Introduction to RNAP===

'''[[RNA polymerase]]''' (RNAP) is a molecular machine that copies DNA into RNA and is found in every living organism. The bacterial RNAP complex consists of six subunits (ββ’α2ωσ) and three channels. RNAP initially binds to DNA at the promoter, forming the closed complex<ref name='genetics'>Snyder, L. & Champness, W. (2007). Molecular genetics of bacteria (3rd ed.). Washington, D.C.: ASM Press.</ref>. The DNA surrounding the promoter sequence unwinds and forms the open complex (http://www.pingrysmartteam.com/RPo/RPo.htm - please note that different nomenclature is used)<ref>2006 Pingry SMART Team: RNA Polymerase Holoenzyme Open Promoter Complex (Rpo) Jmol Tutorial</ref>. RNAP releases from the promoter and transitions into the elongation complex (EC). The EC moves along the template strand, adding ribonucleotides to the 3’ hydroxyl of the growing RNA transcript. 

This tutorial uses the β’ subunit of the RNAP elongation complex of ''Thermus thermophilus''. The β’ subunit contains structures crucial for transcription, including the sites for ribonucleotide addition and catalysis. Double-stranded DNA enters RNAP through the active site channel, while ribonucleotides (NTPs) enter through the secondary channel. As the downstream DNA (dwDNA) enters, it separates into the template and non-template strands. The template strand forms an approximately 90 degree kink in the active site channel. At the kink, one DNA base pair becomes available for NTP pairing and translocates to the +1 site. An NTP enters the active site and induces conformational change of the trigger loop into the trigger helix. The trigger helix forms a three-helical bundle with the bridge helix. This bundle changes dimensions of the active site and facilitates positioning of the NTP for addition to the growing RNA strand. Upon addition of the nucleotide, the dwDNA and RNA/DNA hybrid translocate through RNAP with stabilization from the rudder. The growing RNA strand is separated by the lid and exits RNAP through the exit channel. The DNA template strand rejoins the non-template strand as it exits the active site channel. 

<qt>file=CrestUWMilwaukee2011-Video1.mp4|width=940|height=560|autoplay=false|controller=true|loop=false</qt><br>
<qt>file=CrestUWMilwaukee2011-Video2.mp4|width=940|height=560|autoplay=false|controller=true|loop=false</qt><br>

===Learning Objectives===

*Examine the bending of DNA in the active site channel
*Determine how ribonucleotides enter the active site
*Address how RNA polymerase discriminates between ribonucleotides and deoxyribonucleotides
*Describe how ribonucleotide triphosphates (NTPs) are oriented correctly in the active site for catalysis
*Evaluate the conformational changes of the trigger loop
*Describe how the trigger helix is involved in catalysis

==Tutorial: β’ Subunit of ''Thermus thermophilus'' RNAP==
<font size='3'>'''DNA Translocation and the RNA/DNA Hybrid'''</font>

<scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_dna_1/1'>DNA</scene> in the active site channel provides the genetic information for RNA transcription. The active site channel is 27 Å wide and accommodates both <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_dwdna_1/1'>downstream DNA</scene> (dwDNA) and an <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_hybrid_1/1'>RNA/DNA hybrid</scene><ref>PMID: 10499798</ref>. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_template_1/3'>DNA template strand</scene> (blue) provides the complementary sequence for the RNA transcript and threads through the active site channel adjacent to the active site. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_nontemplate_1/2'>non-template strand</scene> (dark blue), or coding strand, is held away from the active site by the clamp helices and rudder. 

The template strand is kinked at the junction between the dwDNA and RNA/DNA hybrid<ref name='elongation'>PMID: 17581590</ref>. The lone unpaired acceptor template base at the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_kink_1/2'>+1 site</scene> is located at the kink<ref name='elongation' />. The base pair at the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_plus2site_1/2'>+2 site</scene> is distorted<ref name='elongation' />. Upstream of the kink is the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_hybrid_1/1'>RNA/DNA hybrid</scene>. This hybrid structure is comprised of the template strand and the complementary RNA transcript connected by hydrogen bonds. The most recently formed hybrid bond is located at the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_minus1site_1/2'>-1 site</scene><ref name='elongation' />.  

The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_rudder_1/2'>rudder</scene> (coral) stabilizes the dwDNA and upstream RNA/DNA hybrid with numerous sidechain interactions. Two <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_rudderarg_1/1'>arginine sidechains</scene> are shown contacting the dwDNA and RNA/DNA hybrid<ref name='elongation' />. The rudder meets the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_clamp_1/2'>clamp helices</scene> (dark grey) which interact with the σ subunit of RNAP. 

The upstream internal chamber can accommodate a 9-bp RNA/DNA hybrid<ref name='elongation' />. The RNA/DNA hybrid encounters the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lid_1/2'>lid</scene> (light green) that sterically blocks continued elongation<ref name='elongation' />. The lid facilitates <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_lidcleavage_1/1'>cleavage of the hydrogen bond</scene>, releasing the growing RNA transcript into the exit channel. As the bond is cleaved, the template strand moves one position upstream through the active site channel. This process is called translocation. This allows the lone <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_acceptor_1/4'>unpaired template nucleotide</scene> to move into the +1 site adjacent to the active site where nucleotide addition occurs<ref name='elongation' />.

<font size='3'>'''Nucleotide Addition'''</font>

The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_secondary_1/1'>secondary channel</scene>, which is bordered by the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_rim_1/2'>rim helices</scene> (very dark blue), forms the entrance for both ribonucleotides (NTPs) and deoxyribonucleotides (dNTPs) into RNAP. The secondary channel's dimensions are 15 x 20 Å, preventing the entrance of dsDNA<ref name='loading'>PMID: 17581591</ref>. Nucleotides are coupled to a magnesium ion (MgII) as they enter. <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_asn737_1/2'>Asn737</scene> (indigo) evaluates ribose hydroxyl groups in order to discriminate between NTPs and dNTPs<ref name='loading' />. The hydrogen bonds on the incoming NTP must complement those of the acceptor template base. As the NTPs enter, it is proposed that <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_metthr_1/3'>Met1238 and Thr1088</scene> (cyan and magenta) aid in selection and orientation of the cognate NTP<ref name='loading' />. Once the cognate NTP is selected, its alpha and gamma phosphates form temporary phosphate contacts with RNAP near the active site<ref name='loading' />. The nucleotide adopts a relaxed conformation and resists loading into the catalytic position<ref  name='loading' />. This conformation is influenced by the "basic rim gate" consisting of four residues that surround the NTP phosphates<ref  name='loading' />. Two basic rim gate residues, <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_basicgate_1/2'>Arg783 and Arg1029</scene>, are shown (light purple). 

The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_bridge_1/3'>bridge helix</scene> (magenta) separates the active and secondary channels while interacting with the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_trigger_1/2'>trigger helix</scene> (cyan). In the pre-insertion state, the trigger loop has an unstructured conformation<ref  name='loading' />. Loading of the NTP near the active site induces a conformational change in the trigger loop, and it becomes the two-helical trigger helix<ref  name='loading' />. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_trigger2_1/1'>trigger helix</scene> "swings" into the secondary channel and changes the dimensions of the channel to 11 x 11 Å<ref  name='loading' />. This reduction in size prevents diffusion of NTP away from the active site while simultaneously preventing interference from other nucleotides<ref  name='loading' />. The presence of the trigger helix causes the NTP phosphate contacts to change<ref  name='loading' />. All three phosphates contact RNAP and adopt a more rigid conformation<ref  name='loading' />. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_ntp_1/2'>NTP</scene> is now ready for catalysis. 

<font size='3'>'''Catalysis'''</font>

The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_activesite_1/4'>active site</scene> consists of three highly conserved aspartate sidechains (Asp739, Asp741, Asp743) chelated to a magnesium ion (MgI) required for catalysis<ref name='loading' />. <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_mgions_1/2'>MgI and MgII</scene> (lime green) chelated to the NTP coordinate positioning of the NTP for catalysis<ref name='lehninger'>Nelson, D. L. & Cox, M. M. (2008). Lehninger principles of biochemistry (5th ed.). New York: W. H. Freeman and Company.
</ref>. The <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_threeprime_1/2'>3' hydroxyl</scene> of the RNA transcript has nucleophilic activity and attacks the alpha-phosphate of the NTP<ref name='lehninger' />. A phosphodiester bond forms between the RNA transcript and the alpha-phosphate, and the beta- and gamma-phosphates leave as a pyrophosphate group<ref name='lehninger' />. After catalysis the RNA/DNA hybrid moves in the <scene name='Beta-Prime_Subunit_of_Bacterial_RNA_Polymerase/2o5j_minus1site_1/2'>-1 site</scene>, and the ribonucleotide in this bond provides the 3’ hydroxyl for the next incoming NTP<ref name='elongation' />.

===Nucleotide Addition Cycle===

<qt>file=CrestUWMilwaukee2011-Video3.mp4|width=940|height=560|autoplay=false|controller=true|loop=false</qt><br>

An animation showing the conformational changes undergone by the trigger loop/helix when switching from the pre-insertion complex to the insertion complex can currently be found at http://www.molmovdb.org/cgi-bin/morph.cgi?ID=807081-19674. This animation was designed by Mark Hoelzer of the Center for BioMolecular Modeling at MSOE. The conformational change animation is an interpretation of static models, but does not represent the actual conformational change.

===Challenge Questions===
*Why does DNA experience a 90 degree bend in the active site channel? 
*What are the functions of the magnesium ion in the active site and the magnesium ion coupled to the incoming NTP? What are they coordinating? 
*What experiments could prove the ribonucleotide discrimination function of β'Asn737?
*What experimental evidence could confirm that the trigger loop to trigger helix conformational change is involved in catalysis?

==2011 UW-Milwaukee CREST Team==

===Team Members===
Catherine L Dornfeld, Christopher Hanna and Jason Slaasted

===Abstract===

RNA polymerase (RNAP) is an information-processing molecular machine that copies DNA into RNA. It is a multi-subunit complex found in every living organism. Bacterial RNAP contains six subunits (ββ’α2ωσ). This model focuses on the β’ subunit of RNAP elongation complex (EC) of ''Thermus thermophilus'' that contains the active site sequence and several structures involved in the catalytic mechanism: the aspartate residues, the magnesium ions, the bridge helix, and the trigger helix. The active site channel accommodates double stranded DNA (dwDNA) and an RNA/DNA hybrid. The secondary channel, which is bordered by the rim helices, allows nucleotides (NTPs) to enter the active site. The exit channel guides the growing RNA transcript out of the complex. The DNA template strand becomes kinked as it moves through the active site channel and is separated from the non-template strand. This kink allows one dNTP at a time to become available for nucleotide addition once it translocates to the +1 site. The bridge helix (BH) and trigger loop (TL) work together as a “swinging gate” to enhance the catalytic action by facilitating NTP addition. In the crystal structure of the EC without NTP in the active site, the TL (β’ 1236-1265) is unstructured. In the EC crystal structure with a non-hydrolysable nucleotide (AMPcPP), the TL folds into two anti-parallel helices (trigger helix, TH) that interact with the adjacent BH to create a three-helical bundle forming a catalytically active complex. The other structures that are functionally important in the β’ subunit are the lid (β’ 525-539) that cleaves the RNA/DNA hybrid, directing the newly formed RNA out through the exit channel, and the rudder(β’ 582-602) that helps to stabilize the DNA helix and the RNA/DNA hybrid in the active site channel. The clamp helices interact with the σ subunit of RNAP.

===Poster===

[[Image:UWMFinal.jpg|Catherine L Dornfeld| 350px]]

===Acknowledgments===
*Steven Forst, Ph.D., University of Wisconsin-Milwaukee
*Rick Gourse, Ph.D., University of Wisconsin-Madison
*MSOE Center for BioMolecular Modeling: Mark Hoelzer, Margaret Franzen, Ph.D. and Tim Herman, Ph.D. 
*NSF CREST Program

==References==
<references />

</StructureSection>