User:Ketan Mathavan/Sandbox 1: Difference between revisions

(One intermediate revision by the same user not shown)

Line 9:

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The C-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The N-terminal <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, intercalating <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and AT-recognition <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site ~~(Fig.1)~~ (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

== References ==

Line 16:

#Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]

#Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]

== HELP! ==

I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!

@@ Line 9: / Line 9: @@
 Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> (PDB: 3SPA)</scene>. Recent crystallization of this enzyme by [http://www.ncbi.nlm.nih.gov/pubmed/21947009 Temiakov et al.] has revealed structural similarity between the two polymerases. The <font color =gray> C-terminal </font> <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>domain</scene> contains the active site for RNA synthesis. The <font color=magenta> N-terminal </font> <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'> domain, </scene>(NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the <font color=red> specificity </font> <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>, <font color=orange> intercalating </font> <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene> , and <font color=blue> AT-recognition </font> <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>loop</scene>.
-One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (Fig.1) (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.
+One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.
 == References ==
@@ Line 16: / Line 16: @@
 #Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). [http://www.ncbi.nlm.nih.gov/pubmed/7599198 Pubmed]
 #Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠ[http://www.ncbi.nlm.nih.gov/pubmed/19945377 Pubmed]
+== HELP! ==
+I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.
+If there is anyone that may know a remedy for this problem, please contact kmathavan@mcb.umass.edu. Thank you!