6YI2 | pdb_00006yi2

UvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor domain.

• PDB DOI: https://doi.org/10.2210/pdb6YI2/pdb
• BMRB: 50218

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-31 Released: 2020-10-21 
• Deposition Author(s): Kawale, A.A., Burmann, B.B.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Literature

UvrD helicase-RNA polymerase interactions are governed by UvrD's carboxy-terminal Tudor domain.

Kawale, A.A., Burmann, B.M.

(2020) Commun Biol 3: 607-607

• PubMed: 33097771 
• DOI: https://doi.org/10.1038/s42003-020-01332-2
• Primary Citation Related Structures: 
  6YHZ, 6YI2


• PubMed Abstract: 
  

  All living organisms have to cope with the constant threat of genome damage by UV light and other toxic reagents. To maintain the integrity of their genomes, organisms developed a variety of DNA repair pathways. One of these, the Transcription Coupled DNA-Repair (TCR) pathway, is triggered by stalled RNA Polymerase (RNAP) complexes at DNA damage sites on actively transcribed genes. A recently elucidated bacterial TCR pathway employs the UvrD helicase pulling back stalled RNAP complexes from the damage, stimulating recruitment of the DNA-repair machinery. However, structural and functional aspects of UvrD's interaction with RNA Polymerase remain elusive. Here we used advanced solution NMR spectroscopy to investigate UvrD's role within the TCR, identifying that the carboxy-terminal region of the UvrD helicase facilitates RNAP interactions by adopting a Tudor-domain like fold. Subsequently, we functionally analyzed this domain, identifying it as a crucial component for the UvrD-RNAP interaction besides having nucleic-acid affinity.

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Organizational Affiliation: 
• Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, 40530, Sweden.
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, 40530, Sweden.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, 40530, Sweden. [e-mail].
Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, 40530, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 8.45 kDa 
• Atom Count: 593 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase	A	76	Escherichia coli	Mutation(s): 0  Gene Names: uvrD, ACU57_06555 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P03018 (Escherichia coli (strain K12)) Explore P03018  Go to UniProtKB:  P03018

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Kawale, A.A., Burmann, B.B.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-04721
Knut and Alice Wallenberg Foundation	Sweden	2016.0163

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2020-11-18
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-06-19
  Changes: Data collection, Database references