6LWF

Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing guanidinohydantoin (Gh)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes.

Liu, M.Zhang, J.Zhu, C.Zhang, X.Xiao, W.Yan, Y.Liu, L.Zeng, H.Gao, Y.Q.Yi, C.

(2021) Nat Commun 12: 4108-4108

  • DOI: https://doi.org/10.1038/s41467-021-24431-y
  • Primary Citation of Related Structures:  
    6LWA, 6LWB, 6LWC, 6LWD, 6LWF, 6LWG, 6LWH, 6LWI, 6LWJ, 6LWK, 6LWL, 6LWM, 6LWN, 6LWO, 6LWP, 6LWQ, 6LWR

  • PubMed Abstract: 

    DNA glycosylases must distinguish the sparse damaged sites from the vast expanse of normal DNA bases. However, our understanding of the nature of nucleobase interrogation is still limited. Here, we show that hNEIL1 (human endonuclease VIII-like 1) captures base lesions via two competing states of interaction: an activated state that commits catalysis and base excision repair, and a quarantine state that temporarily separates and protects the flipped base via auto-inhibition. The relative dominance of the two states depends on key residues of hNEIL1 and chemical properties (e.g. aromaticity and hydrophilicity) of flipped bases. Such a DNA repair mechanism allows hNEIL1 to recognize a broad spectrum of DNA damage while keeps potential gratuitous repair in check. We further reveal the molecular basis of hNEIL1 activity regulation mediated by post-transcriptional modifications and provide an example of how exquisite structural dynamics serves for orchestrated enzyme functions.


  • Organizational Affiliation

    Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endonuclease 8-like 1
A, D
295Homo sapiensMutation(s): 2 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96FI4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)P*GP*TP*CP*TP*AP*C)-3')
B, E
13Escherichia coli
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
C, F
13Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.604α = 90
b = 142.564β = 90
c = 71.074γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91953201
National Natural Science Foundation of China (NSFC)China21825701

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description