8FTJ | pdb_00008ftj

Crystal structure of human NEIL1 (P2G (242K) C(delta)100) glycosylase bound to DNA duplex containing urea

• PDB DOI: https://doi.org/10.2210/pdb8FTJ/pdb
• NAKB: 8FTJ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-12 Released: 2023-04-26 
• Deposition Author(s): Tomar, R., Sharma, P., Harp, J.M., Egli, M., Stone, M.P.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase.

Tomar, R., Minko, I.G., Sharma, P., Kellum, A.H., Lei, L., Harp, J.M., Iverson, T.M., Lloyd, R.S., Egli, M., Stone, M.P.

(2023) Nucleic Acids Res 51: 3754-3769

• PubMed: 37014002 
• DOI: https://doi.org/10.1093/nar/gkad164
• Primary Citation Related Structures: 
  8FTJ


• PubMed Abstract: 
  

  The N-(2-deoxy-d-erythro-pentofuranosyl)-urea DNA lesion forms following hydrolytic fragmentation of cis-5R,6S- and trans-5R,6R-dihydroxy-5,6-dihydrothymidine (thymine glycol, Tg) or from oxidation of 7,8-dihydro-8-oxo-deoxyguanosine (8-oxodG) and subsequent hydrolysis. It interconverts between α and β deoxyribose anomers. Synthetic oligodeoxynucleotides containing this adduct are efficiently incised by unedited (K242) and edited (R242) forms of the hNEIL1 glycosylase. The structure of a complex between the active site unedited mutant CΔ100 P2G hNEIL1 (K242) glycosylase and double-stranded (ds) DNA containing a urea lesion reveals a pre-cleavage intermediate, in which the Gly2 N-terminal amine forms a conjugate with the deoxyribose C1' of the lesion, with the urea moiety remaining intact. This structure supports a proposed catalytic mechanism in which Glu3-mediated protonation of O4' facilitates attack at deoxyribose C1'. The deoxyribose is in the ring-opened configuration with the O4' oxygen protonated. The electron density of Lys242 suggests the 'residue 242-in conformation' associated with catalysis. This complex likely arises because the proton transfer steps involving Glu6 and Lys242 are hindered due to Glu6-mediated H-bonding with the Gly2 and the urea lesion. Consistent with crystallographic data, biochemical analyses show that the CΔ100 P2G hNEIL1 (K242) glycosylase exhibits a residual activity against urea-containing dsDNA.

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Organizational Affiliation: 
• Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Station B Box 351822, Nashville, TN 37235, USA.
Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA.
Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
Department of Biochemistry, School of Medicine, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, USA.
Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 41.99 kDa 
• Atom Count: 2,793 
• Modeled Residue Count: 289 
• Deposited Residue Count: 323 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease 8-like 1	A	297	Homo sapiens	Mutation(s): 1  Gene Names: NEIL1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FI4 (Homo sapiens) Explore Q96FI4  Go to UniProtKB:  Q96FI4
PHAROS:  Q96FI4 GTEx:  ENSG00000140398

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*CP*CP*AP*UDV*GP*TP*CP*TP*AP*CP)-3')	B [auth D]	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*GP*G)-3')	C [auth F]	13	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.662	α = 90
b = 83.662	β = 90
c = 130.442	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Tomar, R., Sharma, P., Harp, J.M., Egli, M., Stone, M.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 ES-029357

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-05-17
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary