5Y7G

Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease.

Jin, H.Roy, U.Lee, G.Scharer, O.D.Cho, Y.

(2018) J. Biol. Chem. 293: 6482-6496

  • DOI: 10.1074/jbc.RA118.002171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nucl ...

    DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway. Recent structural studies have proposed two different mechanistic features for ICL unhooking by human FAN1: a specific basic pocket that recognizes the terminal phosphate of a 1-nucleotide (nt) 5' flap or FAN1 dimerization. Herein, we show that despite lacking these features, Pseudomonas aeruginosa FAN1 ( Pa FAN1) cleaves substrates at ∼3-nt intervals and resolves ICLs. Crystal structures of Pa FAN1 bound to various DNA substrates revealed that its conserved basic Arg/Lys patch comprising Arg-228 and Lys-260 recognizes phosphate groups near the 5' terminus of a DNA substrate with a 1-nt flap or a nick. Substitution of Lys-260 did not affect Pa FAN1's initial endonuclease activity but significantly decreased its subsequent exonuclease activity and ICL unhooking. The Arg/Lys patch also interacted with phosphates at a 3-nt gap, and this interaction could drive movement of the scissile phosphates into the Pa FAN1-active site. In human FAN1, the ICL-resolving activity was not affected by individual disruption of the Arg/Lys patch or basic pocket. However, simultaneous substitution of both FAN1 regions significantly reduced its ICL-resolving activity, suggesting that these two basic regions play a complementary role in ICL repair. On the basis of these findings, we propose a conserved role for two basic regions in FAN1 to guide ICL unhooking and to maintain genomic stability.


    Organizational Affiliation

    the Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea.,the Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, South Korea, and.,From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea, yunje@postech.ac.kr.,the Departments of Chemistry and Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794.,the Department of Biology, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea.,From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fanconi-associated nuclease 1 homolog
A, B, C
580Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: fan1
EC: 3.1.4.1
Find proteins for Q9I2N0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I2N0
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')D,F,H10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')E,G,I24synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')J,L,N14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 140.290α = 90.00
b = 143.258β = 90.00
c = 172.712γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data processing
HKL-2000data collection
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-08-17 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Cho, Y., Jin, H.

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references, Structure summary