4Q48 | pdb_00004q48

Structure of the RecQ Catalytic Core from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb4Q48/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-14 Released: 2015-05-20 
• Deposition Author(s): Chen, S.C., Yang, C.S., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility.

Chen, S.C., Huang, C.H., Yang, C.S., Way, T.D., Chang, M.C., Chen, Y.

(2014) Biomed Res Int 2014: 342725-342725

• PubMed: 25243132 
• DOI: https://doi.org/10.1155/2014/342725
• Primary Citation Related Structures: 
  4Q47, 4Q48


• PubMed Abstract: 
  

  RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ from Deinococcus radiodurans (DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of the E. coli RecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

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Organizational Affiliation: 
• Department of Biotechnology, Hungkuang University, Taichung 433, Taiwan ; Taiwan Advance Biopharm (TABP), Inc., Xizhi City, New Taipei City 221, Taiwan.
Department of Biotechnology, Hungkuang University, Taichung 433, Taiwan ; Taiwan Advance Biopharm (TABP), Inc., Xizhi City, New Taipei City 221, Taiwan ; Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan.
Department of Biological Science and Technology, College of Life Sciences, China Medical University, Taichung 40402, Taiwan.
Department of Nutrition, Hungkuang University, Taichung 433, Taiwan.
Department of Biotechnology, Hungkuang University, Taichung 433, Taiwan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.95 kDa 
• Atom Count: 7,841 
• Modeled Residue Count: 1,001 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase RecQ	A, B	525	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_1289 EC: 5.6.2.4
UniProt
Find proteins for Q9RUU2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUU2  Go to UniProtKB:  Q9RUU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.791	α = 90
b = 98.528	β = 90
c = 152.88	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Chen, S.C., Yang, C.S., Chen, Y.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description