6SEI

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.

Gaur, V.Ziajko, W.Nirwal, S.Szlachcic, A.Gapinska, M.Nowotny, M.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz842
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-selective endonucleases cleave branched DNA substrates. Slx1 is unique among structure-selective nucleases because it can cleave all branched DNA structures at multiple sites near the branch point. The mechanism behind this broad range of a ...

    Structure-selective endonucleases cleave branched DNA substrates. Slx1 is unique among structure-selective nucleases because it can cleave all branched DNA structures at multiple sites near the branch point. The mechanism behind this broad range of activity is unknown. The present study structurally and biochemically investigated fungal Slx1 to define a new protein interface that binds the non-cleaved arm of branched DNAs. The DNA arm bound at this new site was positioned at a sharp angle relative to the arm that was modeled to interact with the active site, implying that Slx1 uses DNA bending to localize the branch point as a flexible discontinuity in DNA. DNA binding at the new interface promoted a disorder-order transition in a region of the protein that was located in the vicinity of the active site, potentially participating in its formation. This appears to be a safety mechanism that ensures that DNA cleavage occurs only when the new interface is occupied by the non-cleaved DNA arm. Models of Slx1 that interacted with various branched DNA substrates were prepared. These models explain the way in which Slx1 cuts DNA toward the 3' end away from the branch point and elucidate the unique ability of Slx1 to cleave various DNA structures.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Structure-specific endonuclease subunit SLX1
A, C
324Thielavia terrestris (strain ATCC 38088 / NRRL 8126)Mutation(s): 1 
Gene Names: SLX1
EC: 3.1.-.-
Find proteins for G2QV68 (Thielavia terrestris (strain ATCC 38088 / NRRL 8126))
Go to UniProtKB:  G2QV68
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Structure-specific endonuclease subunit SLX4
B, D
104Thielavia terrestrisMutation(s): 0 
Gene Names: SLX4
Find proteins for A0A3S4CYR8 (Thielavia terrestris)
Go to Gene View: SLX4
Go to UniProtKB:  A0A3S4CYR8
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (32-MER)E33synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.075α = 90.00
b = 92.700β = 91.60
c = 93.251γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098022

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references