3Q8L

Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap DNA, SM3+, and K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.319 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily.

Tsutakawa, S.E.Classen, S.Chapados, B.R.Arvai, A.S.Finger, L.D.Guenther, G.Tomlinson, C.G.Thompson, P.Sarker, A.H.Shen, B.Cooper, P.K.Grasby, J.A.Tainer, J.A.

(2011) Cell 145: 198-211

  • DOI: 10.1016/j.cell.2011.03.004
  • Primary Citation of Related Structures:  3Q8K, 3Q8M

  • PubMed Abstract: 
  • Flap endonuclease (FEN1), essential for DNA replication and repair, removes RNA and DNA 5' flaps. FEN1 5' nuclease superfamily members acting in nucleotide excision repair (XPG), mismatch repair (EXO1), and homologous recombination (GEN1) paradoxical ...

    Flap endonuclease (FEN1), essential for DNA replication and repair, removes RNA and DNA 5' flaps. FEN1 5' nuclease superfamily members acting in nucleotide excision repair (XPG), mismatch repair (EXO1), and homologous recombination (GEN1) paradoxically incise structurally distinct bubbles, ends, or Holliday junctions, respectively. Here, structural and functional analyses of human FEN1:DNA complexes show structure-specific, sequence-independent recognition for nicked dsDNA bent 100° with unpaired 3' and 5' flaps. Above the active site, a helical cap over a gateway formed by two helices enforces ssDNA threading and specificity for free 5' ends. Crystallographic analyses of product and substrate complexes reveal that dsDNA binding and bending, the ssDNA gateway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the two-metal-ion active site. Superfamily conserved motifs bind and open dsDNA; direct the target region into the helical gateway, permitting only nonbase-paired oligonucleotides active site access; and support a unified understanding of superfamily substrate specificity.


    Organizational Affiliation

    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flap endonuclease 1
A
341Homo sapiensGene 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')D18N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')E12N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')F7N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

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Download CCD File 
A
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.319 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.161 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.140α = 90.00
b = 105.140β = 90.00
c = 104.050γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance