9NZC | pdb_00009nzc

Crystal structure of AfNth1:Tg-DNA duplex complex in a pre-intermediate state

• PDB DOI: https://doi.org/10.2210/pdb9NZC/pdb
• NAKB: 9NZC

• Classification: LYASE/DNA
• Organism(s): Archaeoglobus fulgidus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-31 Released: 2026-04-15 
• Deposition Author(s): Syed, A., Arvai, A.S., Tsai, C.L., Tainer, J.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.280 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

A unified catalytic mechanism in bifunctional DNA glycosylases with an evolutionarily conserved aspartate-lysine dyad.

Syed, A., Serafim, L.F., Arvai, A.S., Minko, I.G., Tang, H.Y.H., Huffman, J.L., Mol, C.D., Hitomi, K., Sarker, A.H., Parikh, S., Tsai, C.L., Bacolla, A., Shin, D.S., Cunningham, R.P., Iwai, S., Chowdhury, D., Lloyd, R.S., Ivanov, I., Tainer, J.A.

(2026) Nat Commun 

• PubMed: 42457729 
• DOI: https://doi.org/10.1038/s41467-026-75471-1
• Primary Citation Related Structures: 
  10MN, 9NZ8, 9NZ9, 9NZA, 9NZC, 9NZD, 9O00, 9O01, 9O02, 9O03


• PubMed Abstract: 
  

  Bifunctional glycosylases, OGG1 for purines and NTH1 for pyrimidines, repair oxidized DNA bases via consecutive glycosylase and AP-lyase reactions, yet their catalytic relationships and lyase activity's biological relevance remain unresolved. Here, we solved crystal structures of archaeal and human Ogg1 and Nth1 captured in key damage-recognition and catalysis-ready states, complemented by ab initio molecular dynamics simulations of their complete reaction trajectories. We thereby define a unified catalytic mechanism for OGG1 and NTH1 conserved over three billion years, distinct from the canonical oxocarbenium-ion mechanism of monofunctional glycosylases. While divergent in their oxidized substrate recognition, their chemistry converged on ribose protonation and ring opening that precede the deglycosylation step. Acid-base catalysis mediated by a conserved aspartate-lysine dyad lowers the C-N bond cleavage barrier, while the excised 8-oxoG base in OGG1 or a conserved aspartate in NTH1 facilitates the AP-lyase reaction. Moreover, structures of human OGG1 bound to product DNA and to product DNA plus a potent small-molecule agonist F51, within the catalytic pocket, reveal that agonists accelerate enzyme turnover by promoting product release. Together, these findings clarify the catalytic logic of bifunctional glycosylases, enabling the development of chemical tools to interrogate lyase activity and therapeutics for oxidative damage in cancer and aging.

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Organizational Affiliation: 
• Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. [e-mail].
Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. [e-mail].
Department of Chemistry, Georgia State University, Atlanta, GA, USA.
The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.
Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA.
Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Graduate School of Engineering Science, Osaka University, Osaka, Japan.
Biological Systems and Engineering, Lawrence Berkeley National Lab, Berkeley, CA, USA.
Department of Biological Sciences, University at Albany-State University of New York, Albany, NY, USA.
Frontiers of Innovative Research in Science and Technology, Konan University, Kobe, Hyogo, Japan.
Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
Department of Chemistry, Georgia State University, Atlanta, GA, USA. [e-mail].
Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. [e-mail].
The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.08 kDa 
• Atom Count: 4,330 
• Modeled Residue Count: 464 
• Deposited Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease III	A, D	209	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: nth, AF_1692 EC: 4.2.99.18
UniProt
Find proteins for O28581 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28581  Go to UniProtKB:  O28581

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')	B, E	13	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*CP*GP*AP*(CTG)P*AP*CP*GP*CP*CP*A)-3')	C, F	13	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	G [auth A], H [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.280 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.329	α = 90
b = 107.329	β = 90
c = 119.587	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Syed, A., Arvai, A.S., Tsai, C.L., Tainer, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA220430

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release
  
• Version 1.1: 2026-08-05
  Changes: Database references