5Y7G

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

Summary for 5Y7G

• Entry DOI: 10.2210/pdb5y7g/pdb
• Descriptor: Fanconi-associated nuclease 1 homolog, DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3'), 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'), ... (5 entities in total)
• Functional Keywords: nuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); More
• Total number of polymer chains: 12
• Total formula weight: 244990.94

Authors

Cho, Y.,Jin, H. (deposition date: 2017-08-17, release date: 2018-03-14, Last modification date: 2023-11-22)

Primary citation

Jin, H.,Roy, U.,Lee, G.,Scharer, O.D.,Cho, Y.
Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease.
J. Biol. Chem., 293:6482-6496, 2018

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. 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, FAN1 (FAN1) cleaves substrates at ∼3-nt intervals and resolves ICLs. Crystal structures of 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 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 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.

PubMed: 29514982
DOI: 10.1074/jbc.RA118.002171

Experimental method

X-RAY DIFFRACTION (3.4 Å)