4S20

Structural basis for transcription reactivation by RapA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for transcription reactivation by RapA.

Liu, B.Zuo, Y.Steitz, T.A.

(2015) Proc Natl Acad Sci U S A 112: 2006-2010

  • DOI: 10.1073/pnas.1417152112
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNA polymerase (RNAP) loses activity during transcription as it stalls at various inactive states due to erratic translocation. Reactivation of these stalled RNAPs is essential for efficient RNA synthesis. Here we report a 4.7-Å resolution crystal st ...

    RNA polymerase (RNAP) loses activity during transcription as it stalls at various inactive states due to erratic translocation. Reactivation of these stalled RNAPs is essential for efficient RNA synthesis. Here we report a 4.7-Å resolution crystal structure of the Escherichia coli RNAP core enzyme in complex with ATPase RapA that is involved in reactivating stalled RNAPs. The structure reveals that RapA binds at the RNA exit channel of the RNAP and makes the channel unable to accommodate the formation of an RNA hairpin. The orientation of RapA on the RNAP core complex suggests that RapA uses its ATPase activity to propel backward translocation of RNAP along the DNA template in an elongation complex. This structure provides insights into the reactivation of stalled RNA polymerases and helps support ATP-driven backward translocation as a general mechanism for transcriptional regulation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, and Department of Chemistry, Yale University, New Haven, CT 06520 thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'D, I1416Escherichia coliMutation(s): 0 
Gene Names: rpoCO3O_01425
EC: 2.7.7.6
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase-associated protein RapAK, L974Escherichia coliMutation(s): 1 
Gene Names: rapAhepAyabAb0059JW0058
EC: 3.6.4
Find proteins for P60240 (Escherichia coli (strain K12))
Explore P60240 
Go to UniProtKB:  P60240
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alphaA, B, F, G329Escherichia coliMutation(s): 0 
Gene Names: rpoAECDH10B_3470
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaC, H1342Escherichia coliMutation(s): 0 
Gene Names: rpoBO3K_23925
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omegaE, J90Escherichia coliMutation(s): 0 
Gene Names: rpoZO3O_25075
EC: 2.7.7.6
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganism
5'-D(P*AP*CP*GP*AP*CP*TP*GP*AP*GP*CP*CP*GP*AP*TP*G)-3'M, O15N/A
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Entity ID: 7
MoleculeChainsLengthOrganism
5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3'N, P9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
D, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
D, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 336.09α = 90
b = 158.93β = 101.28
c = 255.01γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-03-04
    Changes: Database references