5ZOE

Crystal Structure of D181A hFen1 in complex with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1.

Xu, H., Shi, R., Han, W., Cheng, J., Xu, X., Cheng, K., Wang, L., Tian, B., Zheng, L., Shen, B., Hua, Y., Zhao, Y.

(2018) Nucleic Acids Res. 46: 11315-11325

  • DOI: 10.1093/nar/gky911
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human flap endonuclease 1 (hFEN1) is a structure-specific nuclease essential for DNA replication and repair processes. hFEN1 has 5' flap removal activity, as well as gap endonuclease activity that is critical for restarting stalled replication forks. ...

    Human flap endonuclease 1 (hFEN1) is a structure-specific nuclease essential for DNA replication and repair processes. hFEN1 has 5' flap removal activity, as well as gap endonuclease activity that is critical for restarting stalled replication forks. Here, we report the crystal structures of wild-type and mutant hFEN1 proteins in complex with DNA substrates, followed by mutagenesis studies that provide mechanistic insight into the protein-protein interactions of hFEN1. We found that in an α-helix forming the helical gateway of hFEN1 recognizes the 5' flap prior to its threading into the active site for cleavage. We also found that the β-pin region is rigidified into a short helix in R192F hFEN1-DNA structures, suppressing its gap endonuclease activity and cycle-dependent kinase interactions. Our findings suggest that a single mutation at the primary methylation site can alter the function of hFEN1 and provide insight into the role of the β-pin region in hFEN1 protein interactions that are essential for DNA replication and repair.

    Organizational Affiliation: 

    Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA.,Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, Zhejiang 310029, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flap endonuclease 1
A
333Homo 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(*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')B18synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*CP*GP*TP*CP*C)-3')C8synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*G)-3')D14synthetic construct
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.070α = 90.00
b = 93.830β = 90.00
c = 103.020γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31500656

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release