6SEI

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

• PDB DOI:  https://doi.org/10.2210/pdb6SEI/pdb
• NAKB: 6SEI

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermothielavioides terrestris, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-30 Released: 2019-09-25 
• Deposition Author(s): Gaur, V., Zajko, W., Nirwal, S., Szlachcic, A., Gapinska, M., Nowotny, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.215 

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 47: 11681-11690

• PubMed: 31584081 
• DOI: https://doi.org/10.1093/nar/gkz842
• Primary Citation of Related Structures:  
  6SEH, 6SEI


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 105.63 kDa 
• Atom Count: 6,536 
• Modelled Residue Count: 746 
• Deposited Residue Count: 889 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structure-specific endonuclease subunit SLX1	A, C	324	Thermothielavioides terrestris	Mutation(s): 1  Gene Names: SLX1, THITE_2107775 EC: 3.1
UniProt
Find proteins for G2QV68 (Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126)) Explore G2QV68  Go to UniProtKB:  G2QV68

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structure-specific endonuclease subunit SLX4	B, D	104	Thermothielavioides terrestris	Mutation(s): 0  Gene Names: SLX4, TT172_LOCUS87
UniProt
Find proteins for G2RCY5 (Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126)) Explore G2RCY5  Go to UniProtKB:  G2RCY5

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	E	33	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth A], I [auth C], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	H [auth B], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.075	α = 90
b = 92.7	β = 91.603
c = 93.251	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Gaur, V., Zajko, W., Nirwal, S., Szlachcic, A., Gapinska, M., Nowotny, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098022

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2019-10-23
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2019-12-18
  Changes: Database references