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Structural biology of bacterial RNA polymerase.

Murakami KS - Biomolecules (2015)

Bottom Line: Biol.In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription.In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. kum14@psu.edu.

ABSTRACT
Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

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(a) Three-dimensional representation of the interaction between RNAP and transcription factors. The E. coli RNAP holoenzyme is shown as a molecular surface representation (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange; σ region 1.1: red). Transcription factors binding sites are indicated in double quotation marks and PDB codes of structures are shown in brackets; (b) Three-dimensional representation of the interaction between σ and anti-σ factors. E. coli RNAP holoenzyme is shown as a molecular surface representation, and only the core enzyme is partially transparent (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange). Targets of anti-σ factors are indicated in double quotation marks and PDB codes of structures are shown in brackets.
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biomolecules-05-00848-f002: (a) Three-dimensional representation of the interaction between RNAP and transcription factors. The E. coli RNAP holoenzyme is shown as a molecular surface representation (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange; σ region 1.1: red). Transcription factors binding sites are indicated in double quotation marks and PDB codes of structures are shown in brackets; (b) Three-dimensional representation of the interaction between σ and anti-σ factors. E. coli RNAP holoenzyme is shown as a molecular surface representation, and only the core enzyme is partially transparent (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange). Targets of anti-σ factors are indicated in double quotation marks and PDB codes of structures are shown in brackets.

Mentions: The common core of multi-subunit RNAP in cellular organisms is composed of five subunits that are conserved in all three domains of life. Bacterial RNAP core enzyme is the simplest and best characterized form, consisting of α (two copies), β, β', and ω subunits (Figure 1 and Figure 2a). The core enzyme is responsible for binding to template DNA to synthesize RNA, which is complemented by a σ factor to form a holoenzyme that recognizes the promoter sequence to begin promoter-specific transcription [1,2].


Structural biology of bacterial RNA polymerase.

Murakami KS - Biomolecules (2015)

(a) Three-dimensional representation of the interaction between RNAP and transcription factors. The E. coli RNAP holoenzyme is shown as a molecular surface representation (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange; σ region 1.1: red). Transcription factors binding sites are indicated in double quotation marks and PDB codes of structures are shown in brackets; (b) Three-dimensional representation of the interaction between σ and anti-σ factors. E. coli RNAP holoenzyme is shown as a molecular surface representation, and only the core enzyme is partially transparent (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange). Targets of anti-σ factors are indicated in double quotation marks and PDB codes of structures are shown in brackets.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4496699&req=5

biomolecules-05-00848-f002: (a) Three-dimensional representation of the interaction between RNAP and transcription factors. The E. coli RNAP holoenzyme is shown as a molecular surface representation (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange; σ region 1.1: red). Transcription factors binding sites are indicated in double quotation marks and PDB codes of structures are shown in brackets; (b) Three-dimensional representation of the interaction between σ and anti-σ factors. E. coli RNAP holoenzyme is shown as a molecular surface representation, and only the core enzyme is partially transparent (α subunits: white; β subunit: cyan; β’ subunit: pink; ω subunit: gray; σ70: orange). Targets of anti-σ factors are indicated in double quotation marks and PDB codes of structures are shown in brackets.
Mentions: The common core of multi-subunit RNAP in cellular organisms is composed of five subunits that are conserved in all three domains of life. Bacterial RNAP core enzyme is the simplest and best characterized form, consisting of α (two copies), β, β', and ω subunits (Figure 1 and Figure 2a). The core enzyme is responsible for binding to template DNA to synthesize RNA, which is complemented by a σ factor to form a holoenzyme that recognizes the promoter sequence to begin promoter-specific transcription [1,2].

Bottom Line: Biol.In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription.In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. kum14@psu.edu.

ABSTRACT
Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

Show MeSH