RapA, a Swi2/Snf2 protein

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Crystal structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription (3dmq)

Publication Abstract from PubMed

RapA, as abundant as sigma70 in the cell, is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein with ATPase activity. It stimulates RNAP recycling during transcription. We report a structure of RapA that is also a full-length structure for the entire Swi2/Snf2 family. RapA contains seven domains, two of which exhibit novel protein folds. Our model of RapA in complex with ATP and double-stranded DNA (dsDNA) suggests that RapA may bind to and translocate on dsDNA. Our kinetic template-switching assay shows that RapA facilitates the release of sequestered RNAP from a posttranscrption/posttermination complex for transcription reinitiation. Our in vitro competition experiment indicates that RapA binds to core RNAP only but is readily displaceable by sigma70. RapA is likely another general transcription factor, the structure of which provides a framework for future studies of this bacterial Swi2/Snf2 protein and its important roles in RNAP recycling during transcription.

Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription., Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X, Structure. 2008 Sep 10;16(9):1417-27. PMID:18786404

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3dmq is a 2 chains structure of sequences from Escherichia coli k12. Full crystallographic information is available from OCA. The crystallographic asymmetric unit of the solved structure contains 2 monomers of RapA. Toggle sulfate ion on/off.

The biological molecule is a single-chain RapA monomer.

The structure of each RapA monomer contains seven domains and three linkers. The domains and linkers are colored according to Figure 2 of the paper describing the structure. Additionally, the sulfate ion is shown as in Figure 2. Fancy, high-quality cartoons on/off.

The Ntd contains two copies of a Tudor-like fold; the two subdomains are referred to as NtdA and NtdB. The Tudor-like fold is also seen in the transcription factors NusG (1npr,1npp,1m1h,1m1g) and Mfd (TRCF, transcription-repair coupling factor -2eyq), as well as ribosomal protein L24 (1jj2), human survival of motor neuron protein (1g5v), mammalian DNA repair factor 53BP1 (2ig0,2g3r), and putative fission yeast DNA repair factor Crb2 (2fhd).

The domains and linkers represented similar to Figure 1 of the paper describing the structure.

[Note: the following view generates a substantial surface which may take several minutes to calculate. Use one above as an alternative unless you are willing to spend the time. ]The domains and linkers represented much more similar to Figure 1 of the paper describing the structure. Fancy, high-quality cartoons on/off.

RecA-like portion of RapA with the motifs colored as in figure 3 of the paper describing the structure. (RecA-like portion of RapA with the motifs colored and the backbone shown as in figure 3 of the paper describing the structure.)

The sulfate ion is bound to the P loop of Motif I in the structure. Toggle sulfate ion on/off. . Fancy, high-quality cartoons on/off.

RecA-like portion of RapA in the context of the entire structure. Additionally, showing the sulfate ion in this context. Toggle sulfate ion on/off. .

The ATPase core of RapA represented similarly to a portion of Figure 1 of the paper describing the structure. Toggle sulfate ion on/off. . Fancy, high-quality cartoons on/off.

The ATPase core of RapA represented similarly to figure 4 of the paper describing the structure. Toggle sulfate ion on/off. .

[Note: the following view generates a substantial surface which may take several minutes to calculate. Use one above as an alternative unless you are willing to spend the time.]ATPase core represented very close to how it is illustrated in figure 4 of the paper describing the structure. Toggle sulfate ion on/off. .

RNA polymerase-associated protein RapA dimer complex with sulfate 3dmq

Drag the structure with the mouse to rotate

Reference

  • Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A, Jin DJ, Ji X. Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure. 2008 Sep 10;16(9):1417-27. PMID:18786404 doi:10.1016/j.str.2008.06.012


Created with the participation of Wayne Decatur.

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