1B43 | pdb_00001b43

FEN-1 FROM P. FURIOSUS

• PDB DOI: https://doi.org/10.2210/pdb1B43/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-01-05 Released: 2000-01-12 
• Deposition Author(s): Hosfield, D.J., Mol, C.D., Shen, B., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.231 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.

Hosfield, D.J., Mol, C.D., Shen, B., Tainer, J.A.

(1998) Cell 95: 135-146

• PubMed: 9778254 
• DOI: https://doi.org/10.1016/s0092-8674(00)81789-4
• Primary Citation Related Structures: 
  1B43


• PubMed Abstract: 
  

  Flap endonuclease (FEN-1) removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. The crystal structure of Pyrococcus furiosus FEN-1, active-site metal ions, and mutational information indicate interactions for the single- and double-stranded portions of the flap DNA substrate and identify an unusual DNA-binding motif. The enzyme's active-site structure suggests that DNA binding induces FEN-1 to clamp onto the cleavage junction to form the productive complex. The conserved FEN-1 C terminus binds proliferating cell nuclear antigen (PCNA) and positions FEN-1 to act primarily as an exonuclease in DNA replication, in contrast to its endonuclease activity in DNA repair. FEN-1 mutations altering PCNA binding should reduce activity during replication, likely causing DNA repeat expansions as seen in some cancers and genetic diseases.

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Organizational Affiliation: 
• Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.6 kDa 
• Atom Count: 5,857 
• Modeled Residue Count: 678 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FEN-1)	A, B	340	Pyrococcus furiosus	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for O93634 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O93634  Go to UniProtKB:  O93634

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.231 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.82	α = 90
b = 122.04	β = 90
c = 134.42	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-12 
Deposition Author(s): Hosfield, D.J., Mol, C.D., Shen, B., Tainer, J.A.

Revision History  

• Version 1.0: 2000-01-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references