5K97

Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.

Tsutakawa, S.E.Thompson, M.J.Arvai, A.S.Neil, A.J.Shaw, S.J.Algasaier, S.I.Kim, J.C.Finger, L.D.Jardine, E.Gotham, V.J.B.Sarker, A.H.Her, M.Z.Rashid, F.Hamdan, S.M.Mirkin, S.M.Grasby, J.A.Tainer, J.A.

(2017) Nat Commun 8: 15855-15855

  • DOI: 10.1038/ncomms15855
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects ...

    DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via 'phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Biology, Tufts University, Medford, Massachusetts 02155, USA.,Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Centre for Chemical Biology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flap endonuclease 1
A
341Homo sapiensMutation(s): 1 
Gene Names: FEN1 (RAD2)
EC: 3.1.-.-
Find proteins for P39748 (Homo sapiens)
Go to Gene View: FEN1
Go to UniProtKB:  P39748
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')D18synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')E11synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')F7synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*T)-3')G5synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SM
Query on SM

Download SDF File 
Download CCD File 
A
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.236α = 90.00
b = 105.236β = 90.00
c = 104.548γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM105404
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA92584

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence