5Y7G

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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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:  
    5Y7G, 5Y7Q, 5Z6W

  • 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 nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway ...

    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 LengthOrganismDetailsImage
Fanconi-associated nuclease 1 homologA, B, C580Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: fan1, 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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I2N0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')D, F, H 10synthetic construct
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
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, I 24synthetic construct
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')J,
K [auth L],
L [auth N]		14synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.29α = 90
b = 143.258β = 90
c = 172.712γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
HKL-2000data scaling
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  (Full details and data files)

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