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Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations.

Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S - Transcription (2015)

Bottom Line: RNA polymerase (RNAP) performs various tasks during transcription by changing its conformational states, which are gradually becoming clarified.A recent study focusing on the conformational transition of RNAP between the ratcheted and tight forms illuminated the structural principles underlying its functional operations.

View Article: PubMed Central - PubMed

Affiliation: a Division of Structural and Synthetic Biology ; RIKEN Center for Life Science Technologies ; Suehiro-cho, Tsurumi-ku , Yokohama , Japan.

ABSTRACT
RNA polymerase (RNAP) performs various tasks during transcription by changing its conformational states, which are gradually becoming clarified. A recent study focusing on the conformational transition of RNAP between the ratcheted and tight forms illuminated the structural principles underlying its functional operations.

Show MeSH
RNAP conformations and points of regulation. Schematic representations of (A) the tight form (with the closed clamp) and (B) the ratcheted form (with the open clamp). The structural elements of RNAP (4) are colored as follows: core module, gray; shelf module, cyan; clamp module, yellow-green; jaw-lobe module (β domains), light orange; BH, purple; TL, green. The active site is represented as an orange sphere. (C) Interaction sites for transcription factors and RNA elements are depicted on the structure of Thermus thermophilus RNAP bound with a Gre protein in the open-clamp ratcheted form (10). The RNAP is shown as a ribbon model, and the Gre protein (a hybrid of GreA and Gfh1 (16)) is shown as a magenta-colored surface model. The β-flap domain is colored light blue. The nucleic acids were modeled based on those in the backtracked complex structure (10), and the DNA template strand, non-template strand, and RNA are colored blue, green, and red, respectively.
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f0001: RNAP conformations and points of regulation. Schematic representations of (A) the tight form (with the closed clamp) and (B) the ratcheted form (with the open clamp). The structural elements of RNAP (4) are colored as follows: core module, gray; shelf module, cyan; clamp module, yellow-green; jaw-lobe module (β domains), light orange; BH, purple; TL, green. The active site is represented as an orange sphere. (C) Interaction sites for transcription factors and RNA elements are depicted on the structure of Thermus thermophilus RNAP bound with a Gre protein in the open-clamp ratcheted form (10). The RNAP is shown as a ribbon model, and the Gre protein (a hybrid of GreA and Gfh1 (16)) is shown as a magenta-colored surface model. The β-flap domain is colored light blue. The nucleic acids were modeled based on those in the backtracked complex structure (10), and the DNA template strand, non-template strand, and RNA are colored blue, green, and red, respectively.

Mentions: The bacterial RNAP core is composed of at least 5 subunits, while the eukaryotic RNAPs I, II, and III comprise 12 or more subunits, and their total masses are over 400 kDa. From bacteria to eukaryotes, RNAP adopts a similar “crab-claw” shape, which can be divided into 4 massive blocks called “modules”.1,2 The central part of RNAP is composed of the “shelf” and “core” modules, which form the primary nucleic-acids-binding channel and the secondary channel, a likely path for the substrate nucleoside triphosphates (NTPs) (Fig. 1A, B). The “clamp” and “jaw-lobe” modules protrude from the shelf and core modules, respectively, to complete the primary channel. The active site is formed in the middle of the primary channel, and includes Mg2+ ions and flexible structural elements, such as the “trigger loop (TL)” and the “bridge helix (BH).”Figure 1.


Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations.

Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S - Transcription (2015)

RNAP conformations and points of regulation. Schematic representations of (A) the tight form (with the closed clamp) and (B) the ratcheted form (with the open clamp). The structural elements of RNAP (4) are colored as follows: core module, gray; shelf module, cyan; clamp module, yellow-green; jaw-lobe module (β domains), light orange; BH, purple; TL, green. The active site is represented as an orange sphere. (C) Interaction sites for transcription factors and RNA elements are depicted on the structure of Thermus thermophilus RNAP bound with a Gre protein in the open-clamp ratcheted form (10). The RNAP is shown as a ribbon model, and the Gre protein (a hybrid of GreA and Gfh1 (16)) is shown as a magenta-colored surface model. The β-flap domain is colored light blue. The nucleic acids were modeled based on those in the backtracked complex structure (10), and the DNA template strand, non-template strand, and RNA are colored blue, green, and red, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581356&req=5

f0001: RNAP conformations and points of regulation. Schematic representations of (A) the tight form (with the closed clamp) and (B) the ratcheted form (with the open clamp). The structural elements of RNAP (4) are colored as follows: core module, gray; shelf module, cyan; clamp module, yellow-green; jaw-lobe module (β domains), light orange; BH, purple; TL, green. The active site is represented as an orange sphere. (C) Interaction sites for transcription factors and RNA elements are depicted on the structure of Thermus thermophilus RNAP bound with a Gre protein in the open-clamp ratcheted form (10). The RNAP is shown as a ribbon model, and the Gre protein (a hybrid of GreA and Gfh1 (16)) is shown as a magenta-colored surface model. The β-flap domain is colored light blue. The nucleic acids were modeled based on those in the backtracked complex structure (10), and the DNA template strand, non-template strand, and RNA are colored blue, green, and red, respectively.
Mentions: The bacterial RNAP core is composed of at least 5 subunits, while the eukaryotic RNAPs I, II, and III comprise 12 or more subunits, and their total masses are over 400 kDa. From bacteria to eukaryotes, RNAP adopts a similar “crab-claw” shape, which can be divided into 4 massive blocks called “modules”.1,2 The central part of RNAP is composed of the “shelf” and “core” modules, which form the primary nucleic-acids-binding channel and the secondary channel, a likely path for the substrate nucleoside triphosphates (NTPs) (Fig. 1A, B). The “clamp” and “jaw-lobe” modules protrude from the shelf and core modules, respectively, to complete the primary channel. The active site is formed in the middle of the primary channel, and includes Mg2+ ions and flexible structural elements, such as the “trigger loop (TL)” and the “bridge helix (BH).”Figure 1.

Bottom Line: RNA polymerase (RNAP) performs various tasks during transcription by changing its conformational states, which are gradually becoming clarified.A recent study focusing on the conformational transition of RNAP between the ratcheted and tight forms illuminated the structural principles underlying its functional operations.

View Article: PubMed Central - PubMed

Affiliation: a Division of Structural and Synthetic Biology ; RIKEN Center for Life Science Technologies ; Suehiro-cho, Tsurumi-ku , Yokohama , Japan.

ABSTRACT
RNA polymerase (RNAP) performs various tasks during transcription by changing its conformational states, which are gradually becoming clarified. A recent study focusing on the conformational transition of RNAP between the ratcheted and tight forms illuminated the structural principles underlying its functional operations.

Show MeSH