6BOG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.

Shaw, G.Gan, J.Zhou, Y.N.Zhi, H.Subburaman, P.Zhang, R.Joachimiak, A.Jin, D.J.Ji, X.

(2008) Structure 16: 1417-1427

  • DOI: 10.1016/j.str.2008.06.012
  • Primary Citation of Related Structures:  
    6BOG

  • PubMed Abstract: 
  • 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, 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.


    Related Citations: 
    • Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES.
      Kakar, S., Fang, X., Lubkowska, L., Zhou, Y.N., Shaw, G.X., Wang, Y.X., Jin, D.J., Kashlev, M., Ji, X.
      (2015) J Biol Chem 290: 23656

    Organizational Affiliation

    Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein RapAA, B968Escherichia coli S88Mutation(s): 0 
Gene Names: rapAECS88_0062
EC: 3.6.4
UniProt
Find proteins for B7MAI2 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MAI2 
Go to UniProtKB:  B7MAI2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.856α = 90
b = 123.856β = 90
c = 187.994γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references