5Z68

Structure of the recombination mediator protein RecF-ATP in RecFOR pathway

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Literature

ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair.

Tang, Q., Liu, Y.P., Shan, H.H., Tian, L.F., Zhang, J.Z., Yan, X.X.

(2018) Sci Rep 8: 2127-2127

  • DOI: 10.1038/s41598-018-20557-0
  • Primary Citation of Related Structures:  
    5Z67, 5Z68, 5Z69

  • PubMed Abstract: 

    • RecF is a principal member of the RecF pathway. It interacts with RecO and RecR to initiate homologous recombination by loading RecA recombinases on single-stranded DNA and displacing single-stranded DNA-binding proteins. As an ATP-binding cassette ATPase, RecF exhibits ATP-dependent dimerization and structural homology with Rad50 and SMC proteins ...

    RecF is a principal member of the RecF pathway. It interacts with RecO and RecR to initiate homologous recombination by loading RecA recombinases on single-stranded DNA and displacing single-stranded DNA-binding proteins. As an ATP-binding cassette ATPase, RecF exhibits ATP-dependent dimerization and structural homology with Rad50 and SMC proteins. However, the mechanism and action pattern of RecF ATP-dependent dimerization remains unclear. Here, We determined three crystal structures of TTERecF, TTERecF-ATP and TTERecF-ATPɤS from Thermoanaerobacter tengcongensis that reveal a novel ATP-driven RecF dimerization. RecF contains a positively charged tunnel on its dimer interface that is essential to ATP binding. Our structural and biochemical data indicate that the Walker A motif serves as a switch and plays a key role in ATP binding and RecF dimerization. Furthermore, Biolayer interferometry assay results showed that the TTERecF interacted with ATP and formed a dimer, displaying a higher affinity for DNA than that of the TTERecF monomer. Overall, our results provide a solid structural basis for understanding the process of RecF binding with ATP and the functional mechanism of ATP-dependent RecF dimerization.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. snow@ibp.ac.cn.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication and repair protein RecFA, B, C, D373Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: recF, TTE0004
UniProt
Find proteins for Q8RDL3 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8RDL3 
Go to UniProtKB:  Q8RDL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RDL3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
T [auth C],
Z [auth D]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
GA [auth D],
L [auth A],
S [auth B],
Y [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.118α = 90
b = 138.821β = 90
c = 179.567γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31400656

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release