RNA polymerase structure

Ebright RH RNA polymerase structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 2000 304 S87. 

Figure 28.1. RNA Polymerase Structures. The three-dimensional structures of RNA polymerases from a prokaryote...

Cheetham, G. M., and Steitz, T. A. 1 999. Structure of a transcribing T7 RNA polymerase initiation complex. Science 286 2305-2309. Ebright, R. H. 2000. RNA polymerase Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. j. Mol. Biol. 304 687—698. 

Cramer, P., et al. Architecture of RNA Polymerase II and Implications for the Transcription Mechanism. Sdmce 288, 640-649 (2000). [Good overview of RNA polymerase structure and function.]... 

Young, B. A., T. M. Gruber, and C. A. Gross. Minimal Machinery of RNA Polymerase Holoenzyme Sufficient for Promoter Melting. Sdence 303, 1382-1384 (2004). [Research article about RNA polymerase structure and function.]... 

Bacteria and archaea contain a single multisubunit RNA polymerase. X-ray crystallographic structures were determined of a bacterial RNA polymerase from Thermus aquaticus at 3.3-A resolution (Darst, 2001 Zhang et al., 1999). Comparison of this bacterial RNA polymerase structure... 

Wang, B., Jones, D. N., Kaine, B. P., and Weiss, M. A. (1998). High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure 6(5), 555-569. 

Protein molecules that have only one chain are called monomeric proteins. But a fairly large number of proteins have a quaternary structure, which consists of several identical polypeptide chains (subunits) that associate into a multimeric molecule in a specific way. These subunits can function either independently of each other or cooperatively so that the function of one subunit is dependent on the functional state of other subunits. Other protein molecules are assembled from several different subunits with different functions for example, RNA polymerase from E. coli contains five different polypeptide chains. 

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

Due to the large amount of DNA present within the nucleus it must be carefully packaged. In the resting cell DNA is tightly compacted around basic histone proteins, excluding the binding of the enzyme RNA polymerase II, which activates the formation of mRNA. This conformation of the chromatin structure... 

Crystal structures of the NS5B polymerase alone and in complexes with nucleotide substrates have been solved and applied to discovery programs (Ago et al. 1999 Bressanelli et al. 2002 Bressanelli et al. 1999 Lesburg et al. 1999 O Farrell et al. 2003). From these studies, HCV polymerase reveals a three-dimensional structure that resembles aright hand with characteristic fingers, palm, and thumb domain, similar to the architectures of the RNA polymerases of other viruses. However, none of these experimental structures contained the ternary initiation complex with nu-cleotide/primer/template, as obtained with HIV RT. Accordingly, HCV initiation models have been built using data from other viral systems in efforts to explain SAR (Kozlov et al. 2006 Yan et al. 2007). 

Lesburg CA, Cable MB, Ferrari E, Hong Z, Mannarino AF, Weber PC (1999) Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site, Nat Struct Biol 6 937-943... 

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

Figure 37-6. The predominant bacterial transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of AT base pairs (top figure). The inverted repeat, when transcribed into RNA, can generate the secondary structure in the RNA transcript shown at the bottom of the figure. Formation of this RNA hairpin causes RNA polymerase to pause and subsequently the p termination factor interacts with the paused polymerase and somehow induces chain termination.

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

Cramer P, Bushnell DA, Kornberg R Structural basis of transcription RNA polymerase II at 2.8 angstrom resolution. Science 2001 292 1863. 

Woychik NA, Hampsey M The RNA polymerase II machinery structure illuminates function. Cell 2002 108 453. 

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