5FDK

Crystal structure of RecU(D88N) in complex with palindromic DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.208 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state.

Khavnekar, S.Dantu, S.C.Sedelnikova, S.Ayora, S.Rafferty, J.Kale, A.

(2017) Nucleic Acids Res. 45: 975-986

  • DOI: 10.1093/nar/gkw1165

  • PubMed Abstract: 
  • Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolu ...

    Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state.


    Organizational Affiliation

    UM-DAE Centre for Excellence in Basic Science, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Holliday junction resolvase RecU
A, B, C, D
199Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: recU (prfA, yppB)
EC: 3.1.22.-
Find proteins for P39792 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39792
Entity ID: 2
MoleculeChainsLengthOrganism
palindromic DNAE,F,G,H12synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.208 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.256 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 144.447α = 90.00
b = 144.447β = 90.00
c = 310.343γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2017-02-08
    Type: Database references