Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution

  title={Structural Basis of Transcription: RNA Polymerase II at 2.8 {\AA}ngstrom Resolution},
  author={Patrick Cramer and David A. Bushnell and Roger D. Kornberg},
  pages={1863 - 1876}
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding… 

Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution

The crystal structure of a T7 RNA polymerase elongation complex shows that incorporation of an 8-base-pair RNA–DNA hybrid into the active site of the enzyme induces a marked rearrangement of the amino-terminal domain, resulting in a structure that provides elements required for stable transcription elongation.

Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution

The crystal structure of the initiating form of Thermus aquaticus RNA polymerase, containing core RNA polymerase (α2ββ′ω) and the promoter specificity σ subunit, has been determined at 4 angstrom

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution

The crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 Å resolution provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

Structural basis for transcription elongation by bacterial RNA polymerase

The 2.5-Å resolution structure of the Thermus thermophilus EC is reported; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate.

The Structure of Bacterial RNA Polymerase

This chapter describes crystal structures of RNA polymerase (RNAP) structures and their implications for understanding the mechanism of transcription and the regulation of key steps in the

Crystal structure of the 14-subunit RNA polymerase I

The crystal structure of Pol I from Saccharomyces cerevisiae at 3.0 Å resolution shows a compact core with a wide DNA-binding cleft and a tightly anchored stalk, and an extended loop mimics the DNA backbone in the clefts and may be involved in regulating Pol I transcription.

Structure and dynamics of RNA polymerase II elongation complex.

Activity Map of the Escherichia coli RNA Polymerase Bridge Helix*

It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which is infer results in conformational changes in RNAP that modify RNAP functionality.

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

The structure of the mammalian Pol II–DSIF elongation complex is determined using cryo-EM and X-ray crystallography to provide insight into the roles of DSIF during mRNA synthesis.

Structure and function of RNA polymerase II.

  • P. Cramer
  • Biology
    Advances in protein chemistry
  • 2004

Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution

The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 Å resolution and protein–nucleic acid contacts help explain DNA and RNA strand contacts, the specificity of RNA synthesis, “abortive cycling” during transcription initiation, and RNA and DNA translocation during transcription elongation.

A structural model of transcription elongation.

The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase and transcript RNA or template DNA onto the x-ray crystal structure and the resulting model provides insight into the functional properties of the transcription complex.

Spatial organization of transcription elongation complex in Escherichia coli.

DNA entry and RNA exit occur close together in the RNA polymerase molecule, suggesting that the three sites constitute a single unit, which explains how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex.

Structure of a transcribing T7 RNA polymerase initiation complex.

The structure of a T7 RNA polymerase (T7 RNAP) initiation complex captured transcribing a trinucleotide of RNA from a 17-base pair promoter DNA containing a 5-nucleotide single-strand template

Protein-RNA interactions in the active center of transcription elongation complex.

Elongation arrest appears to involve the disengagement of the bulk of the active center from the 3' terminus of RNA and the transfer of the terminus into a new protein environment.

Structural basis for initiation of transcription from an RNA polymerase–promoter complex

Although the single-polypeptide-chain RNA polymerase from bacteriophage T7 (T7RNAP), like other RNA polymerases, uses the same mechanism of polymerization as the DNA polymerases, it can also

Functional topography of nascent RNA in elongation intermediates of RNA polymerase.

The results prove that all of the cuts detected within the 14-nt zone are derived from the EC that is denatured during inactivation of the RNases, and suggest that the transcript-RNAP interaction that is required for holding the EC together can be limited to the RNA region involved in the 8- to 10-nt RNA.

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme

The T7 RNA polymerase–T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 Å crystal structure of the complex reveals that lysozyme binds at a site remote