4R8A | pdb_00004r8a

Crystal structure of paFAN1 - 5' flap DNA complex

• PDB DOI: https://doi.org/10.2210/pdb4R8A/pdb
• NAKB: 4R8A

• Classification: Hydrolase/DNA
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-30 Released: 2014-10-29 
• Deposition Author(s): Cho, Y., Gwon, G.H., Kim, Y.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1

Gwon, G.H., Kim, Y.R., Liu, Y., Watson, A.T., Jo, A., Etheridge, T.J., Yuan, F., Zhang, Y., Kim, Y.C., Carr, A.M., Cho, Y.

(2014) Genes Dev 28: 2276-2290

• PubMed: 25319828 
• DOI: https://doi.org/10.1101/gad.248492.114
• Primary Citation Related Structures: 
  4R89, 4R8A


• PubMed Abstract: 
  

  Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

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Organizational Affiliation: 
• Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea;
Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, East Sussex BN1 9RQ, United Kingdom;
Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA;
Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.
Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, South Korea; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.34 kDa 
• Atom Count: 10,652 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,210 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, E [auth F]	559	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA1865 EC: 3.1.4.1
UniProt
Find proteins for Q9I2N0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I2N0  Go to UniProtKB:  Q9I2N0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')	B, F [auth G]	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')	C, G [auth H]	10	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*A)-3')	D, H [auth I]	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.581	α = 90
b = 106.663	β = 89.97
c = 142.18	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Cho, Y., Gwon, G.H., Kim, Y.R.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references