7N3Z | pdb_00007n3z

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain

• PDB DOI: https://doi.org/10.2210/pdb7N3Z/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-02 Released: 2022-09-28 
• Deposition Author(s): Wojtaszek, J.L., Wallace, B.D., Williams, R.S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.

Williams, J.S., Wojtaszek, J.L., Appel, D.C., Krahn, J., Wallace, B.D., Walsh, E., Kunkel, T.A., Williams, R.S.

(2022) Cell Rep 41: 111448-111448

• PubMed: 36198268 
• DOI: https://doi.org/10.1016/j.celrep.2022.111448
• Primary Citation Related Structures: 
  7N3Y, 7N3Z


• PubMed Abstract: 
  

  Topoisomerase 1 (Top1) incises DNA containing ribonucleotides to generate complex DNA lesions that are resolved by APE2 (Apn2 in yeast). How Apn2 engages and processes this DNA damage is unclear. Here, we report X-ray crystal structures and biochemical analysis of Apn2-DNA complexes to demonstrate how Apn2 frays and cleaves 3' DNA termini via a wedging mechanism that facilitates 1-6 nucleotide endonucleolytic cleavages. APN2 deletion and DNA-wedge mutant Saccharomyces cerevisiae strains display mutator phenotypes, cell growth defects, and sensitivity to genotoxic stress in a ribonucleotide excision repair (RER)-defective background harboring a high density of Top1-incised ribonucleotides. Our data implicate a wedge-and-cut mechanism underpinning the broad-specificity Apn2 nuclease activity that mitigates mutagenic and genome instability phenotypes caused by Top1 incision at genomic ribonucleotides incorporated by DNA polymerase epsilon.

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Organizational Affiliation: 
• Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA. Electronic address: [e-mail].
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.45 kDa 
• Atom Count: 3,246 
• Modeled Residue Count: 379 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) endonuclease 2	A	413	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: APN2, ETH1, YBL019W, YBL0443 EC: 3.1 (PDB Primary Data), 3.1.11.2 (UniProt)
UniProt
Find proteins for P38207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38207  Go to UniProtKB:  P38207

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.412	α = 90
b = 46.948	β = 104.213
c = 51.532	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Wojtaszek, J.L., Wallace, B.D., Williams, R.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1Z01ES102765

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2022-10-19
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description