3GP8

Crystal structure of the binary complex of RecD2 with DNA

• PDB DOI:  https://doi.org/10.2210/pdb3GP8/pdb
• NAKB: 3GP8

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


• Deposited: 2009-03-23 Released: 2009-06-16 
• Deposition Author(s): Saikrishnan, K., Cook, N., Wigley, D.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Mechanistic basis of 5'-3' translocation in SF1B helicases.

Saikrishnan, K., Powell, B., Cook, N.J., Webb, M.R., Wigley, D.B.

(2009) Cell 137: 849-859

• PubMed: 19490894 
• DOI: https://doi.org/10.1016/j.cell.2009.03.036
• Primary Citation of Related Structures:  
  3GP8, 3GPL


• PubMed Abstract: 
  

Superfamily 1B (SF1B) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. However, structural analyses to date have focused on how SF1A helicases achieve 3'-5' movement along nucleic acids. We present crystal structures of the complex between the SF1B helicase RecD2 from Deinococcus radiodurans and ssDNA in the presence and absence of an ATP analog. These snapshots of the reaction pathway reveal a nucleotide binding-induced conformational change of the two motor domains that is broadly reminiscent of changes observed in other SF1 and SF2 helicases. Together with biochemical data, the structures point to a step size for translocation of one base per ATP hydrolyzed. Moreover, the structures also reveal a mechanism for nucleic acid translocation in the 5'-3' direction by SF1B helicases that is surprisingly different from that of 3'-5' translocation by SF1A enzymes, and explains the molecular basis of directionality.

---

Related Citations: 

• DNA binding to RecD: role of the 1B domain in SF1B helicase activity.
  Saikrishnan, K., Griffiths, S.P., Cook, N., Court, R., Wigley, D.B.
  (2008) EMBO J 27: 2222

---

Organizational Affiliation: 

Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN63LD, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.68 kDa 
• Atom Count: 4,435 
• Modelled Residue Count: 559 
• Deposited Residue Count: 588 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease V, subunit RecD, putative	A	574	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_1902, recD, recD2 EC: 3.6.4.12
UniProt
Find proteins for Q9RT63 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RT63  Go to UniProtKB:  Q9RT63

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3'	B [auth X]	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.14	α = 90
b = 90.32	β = 90
c = 142.18	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Saikrishnan, K., Cook, N., Wigley, D.B.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description