9LNP | pdb_00009lnp

the hUNG bound to DNA product embedding uridine ribonucleotide

• PDB DOI: https://doi.org/10.2210/pdb9LNP/pdb
• NAKB: 9LNP

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-01-21 Released: 2025-04-16 
• Deposition Author(s): Liu, Y., Zhou, C., Zhan, X., Fan, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Uridine Embedded within DNA is Repaired by Uracil DNA Glycosylase via a Mechanism Distinct from That of Ribonuclease H2.

Fan, C., Zhan, X., Guo, F., Li, Q., Lu, K., Shan, X., Zhou, Y., Ren, M., Greenberg, M.M., Liu, Y., Zhou, C.

(2025) J Am Chem Soc 147: 11574-11583

• PubMed: 40130361 
• DOI: https://doi.org/10.1021/jacs.5c01436
• Primary Citation of Related Structures:  
  9LNP, 9LNQ


• PubMed Abstract: 
  

  Uridine (rU) and 2'-deoxyuridine (dU) are common DNA lesions. dU is repaired through a base excision repair (BER) pathway initiated by uracil DNA glycosylase (UDG), while rU is typically removed from DNA via ribonucleotide excision repair, mediated by RNase H2. In this study, we report that rU is also repaired through the UDG-mediated BER pathway. We found that UDG catalyzes the removal of uracil from rU embedded in DNA, but exhibits no activity toward rU in RNA. Biochemical and crystallographic analyses revealed that the 2'-OH group of rU is effectively accommodated by UDG and directly participates in catalyzing the hydrolysis of the N -glycosidic bond. The abasic site product generated upon removal of uracil from rU by UDG is further processed by downstream BER enzymes to restore undamaged DNA. Our findings suggest that UDG-initiated BER constitutes a previously unrecognized pathway for the repair of rU-specific ribonucleotides. Additionally, we developed a method for selectively quantifying rU content in DNA. Using this method, we determined that rU repair by UDG is not a major pathway in human cells. This discovery expands our understanding of the diverse biological functions of UDG, and inspires further investigation to determine the role of its rU-removal in cells.

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Organizational Affiliation: 
• State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China.
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.
Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 31.28 kDa 
• Atom Count: 2,510 
• Modeled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	C [auth E]	224	Homo sapiens	Mutation(s): 0  Gene Names: UNG, DGU, UNG1, UNG15 EC: 3.2.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens) Explore P13051  Go to UniProtKB:  P13051
PHAROS:  P13051 GTEx:  ENSG00000076248

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*T*(RP5)P*AP*TP*CP*TP*T)-3')	A	9	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3')	B	10	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.93	α = 90
b = 65.29	β = 90
c = 99.53	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Liu, Y., Zhou, C., Zhan, X., Fan, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877065
National Natural Science Foundation of China (NSFC)	China	82111530210
Ministry of Science and Technology (MoST, China)	China	2023YFA0913800

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release