7N8S

LINE-1 endonuclease domain complex with DNA

Summary for 7N8S

• Entry DOI: 10.2210/pdb7n8s/pdb
• Descriptor: LINE-1 retrotransposable element ORF2 protein, DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3'), DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3') (3 entities in total)
• Functional Keywords: endonuclease, non-ltr retrotransposon, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 36250.25

Authors

Korolev, S.,Miller, I. (deposition date: 2021-06-15, release date: 2021-10-13, Last modification date: 2024-10-16)

Primary citation

Miller, I.,Totrov, M.,Korotchkina, L.,Kazyulkin, D.N.,Gudkov, A.V.,Korolev, S.
Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Nucleic Acids Res., 49:11350-11366, 2021

PubMed Abstract: Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1's ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5'-TTTTT/AA-3'. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN's sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes 'compression' near the cleavage site. This provides multiple advantages for L1-EN's role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.

PubMed: 34554261
DOI: 10.1093/nar/gkab826

Experimental method

X-RAY DIFFRACTION (2.79 Å)