5Z6W

Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap with Manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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
  • Structures With Same Primary Citation

  • 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

    From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea, yunje@postech.ac.kr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fanconi-associated nuclease 1 homologA580Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: fan1PA1865
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))
Explore Q9I2N0 
Go to UniProtKB:  Q9I2N0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')H10synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*TP*TP*CP*AP*A)-3')B13synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')C24synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.874α = 90
b = 104.969β = 90
c = 105.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-01-25 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Jin, H., Cho, Y.

Revision History 

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