7N3Y | pdb_00007n3y

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA

PDB DOI: https://doi.org/10.2210/pdb7N3Y/pdb
NAKB: 7N3Y

Classification: HYDROLASE/DNA
Organism(s): Saccharomyces cerevisiae, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

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

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2022.111448
Primary Citation of 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.

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.

Macromolecule Content

Total Structure Weight: 206.38 kDa
Atom Count: 12,821
Modeled Residue Count: 1,534
Deposited Residue Count: 1,704
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) endonuclease 2	A, B, C, D	413	Saccharomyces cerevisiae	Mutation(s): 2 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38207
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPCPCPGPAPAPAPTP(PST)P(PST)P(SC)P(GS)P*(GS))-3')	E, F, G	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPCPGPAPAPAPTPTP(PST)P(SC)P(GS)P(GS)P*(AS))-3')	H	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D]	K [auth B], O [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain K [auth B] Focus chain O [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth D]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain I [auth A] MOL2 format, chain N [auth C] MOL2 format, chain I [auth A] mmCIF format, chain N [auth C] mmCIF format, chain I [auth A]	I [auth A], N [auth C]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain I [auth A] Focus chain N [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]