7N8S | pdb_00007n8s

LINE-1 endonuclease domain complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb7N8S/pdb
• NAKB: 7N8S

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-15 Released: 2021-10-13 
• Deposition Author(s): Korolev, S., Miller, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.322 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.

Miller, I., Totrov, M., Korotchkina, L., Kazyulkin, D.N., Gudkov, A.V., Korolev, S.

(2021) Nucleic Acids Res 49: 11350-11366

• PubMed: 34554261 
• DOI: https://doi.org/10.1093/nar/gkab826
• Primary Citation Related Structures: 
  7N8K, 7N8S, 7N94


• 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.

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Organizational Affiliation: 
• Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
Molsoft LLC, San Diego, CA 92121, USA.
Genome Protection, Inc., Buffalo, NY 14203, USA.
Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.25 kDa 
• Atom Count: 2,527 
• Modeled Residue Count: 262 
• Deposited Residue Count: 268 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LINE-1 retrotransposable element ORF2 protein	A	238	Homo sapiens	Mutation(s): 2  EC: 2.7.7.49 (PDB Primary Data), 3.1.21 (PDB Primary Data)
UniProt
Find proteins for O00370 (Homo sapiens) Explore O00370  Go to UniProtKB:  O00370

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*TP*AP*AP*AP*AP*AP*GP*GP*AP*GP*CP*T)-3')	B [auth D]	15	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*CP*CP*TP*TP*TP*TP*TP*AP*AP*GP*GP*A)-3')	C	15	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.322 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.613	α = 90
b = 91.613	β = 90
c = 229.822	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Korolev, S., Miller, I.

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary