7CD5 | pdb_00007cd5

mAPE1-blunt-ended dsDNA product complex

• PDB DOI: https://doi.org/10.2210/pdb7CD5/pdb
• NAKB: 7CD5

• Classification: HYDROLASE/DNA
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-18 Released: 2021-01-13 
• Deposition Author(s): Liu, T.C., Hsiao, Y.Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.

Liu, T.C., Lin, C.T., Chang, K.C., Guo, K.W., Wang, S., Chu, J.W., Hsiao, Y.Y.

(2021) Nat Commun 12: 601-601

• PubMed: 33504804 
• DOI: https://doi.org/10.1038/s41467-020-20853-2
• Primary Citation Related Structures: 
  7CD5, 7CD6


• PubMed Abstract: 
  

  The exonuclease activity of Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for processing matched/mismatched terminus in various DNA repair pathways and for removing nucleoside analogs associated with drug resistance. To fill in the gap of structural basis for exonucleolytic cleavage, we determine the APE1-dsDNA complex structures displaying end-binding. As an exonuclease, APE1 does not show base preference but can distinguish dsDNAs with different structural features. Integration with assaying enzyme activity and binding affinity for a variety of substrates reveals for the first time that both endonucleolytic and exonucleolytic cleavage can be understood by an induced space-filling model. Binding dsDNA induces RM (Arg176 and Met269) bridge that defines a long and narrow product pocket for exquisite machinery of substrate selection. Our study paves the way to comprehend end-processing of dsDNA in the cell and the drug resistance relating to APE1.

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Organizational Affiliation: 
• Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30068, Taiwan.
Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30068, Taiwan.
Master's and Doctoral Degree Program for Science and Technology of Accelerator Light Sources, National Chiao Tung University, Hsinchu, 30068, Taiwan.
Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan.
Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan.
Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 30068, Taiwan. [e-mail].
Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30068, Taiwan. [e-mail].
Master's and Doctoral Degree Program for Science and Technology of Accelerator Light Sources, National Chiao Tung University, Hsinchu, 30068, Taiwan. [e-mail].
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan. [e-mail].
Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan. [e-mail].
Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 41.84 kDa 
• Atom Count: 2,374 
• Modeled Residue Count: 286 
• Deposited Residue Count: 360 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-(apurinic or apyrimidinic site) endonuclease	B [auth A]	351	Mus musculus	Mutation(s): 0  Gene Names: Apex1, Ape, Apex, Ref1 EC: 3.1 (PDB Primary Data), 3.1.21 (UniProt), 3.1.11.2 (UniProt)
UniProt
Find proteins for P28352 (Mus musculus) Explore P28352  Go to UniProtKB:  P28352

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3')	A [auth B]	9	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.21	α = 90
b = 107.21	β = 90
c = 230.792	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Liu, T.C., Hsiao, Y.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 109-2636-B-009-004

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description