8JYD | pdb_00008jyd

A genetically encoded sensor based on a bacterial DNA ligase

• PDB DOI: https://doi.org/10.2210/pdb8JYD/pdb

• Classification: LIGASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-03 Released: 2024-07-10 
• Deposition Author(s): Chen, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.256 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Quantitative dynamics of intracellular NMN by genetically encoded biosensor.

Chen, L., Wang, P., Huang, G., Cheng, W., Liu, K., Yu, Q.

(2025) Biosens Bioelectron 267: 116842-116842

• PubMed: 39418868 
• DOI: https://doi.org/10.1016/j.bios.2024.116842
• Primary Citation of Related Structures:  
  8JYD


• PubMed Abstract: 
  

  Nicotinamide mononucleotide (NMN) is the direct precursor and a major booster of NAD ⁺ with increasing applications in NAD ⁺ - and aging-related pathologies. However, measuring live cell NMN dynamics was not possible, leaving key questions in NMN uptake and intracellular regulation unanswered. Here we developed genetically encoded bioluminescent and fluorescent sensors to quantify subcellular NMN in live cells by engineering specific NMN-responsive protein scaffolds fused to luciferase and fluorescent proteins. The sensor dissected the multimechanistic uptake of exogenous NMN and nicotinamide riboside (NR) in live cells and further measured the NMN levels across different subcellular compartments, as well as the perturbed NMN/NAD ⁺ ratios by external supplements. Moreover, we measured the NMN regulation by NAD(H) hydrolase Nudts and peroxisomal carrier Pxmp2 and identified Slc25a45 as a potential mitochondrial NMN regulator for its unique fingerprint on the local NMN/NAD ⁺ ratio. Collectively, the genetically encoded sensors provide a useful tool for visualizing NMN metabolism.

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Organizational Affiliation: 
• Sino-European Center of Biomedicine and Health, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
Department of Medical Oncology, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University, 510060, Guangzhou, China. Electronic address: [e-mail].
Sino-European Center of Biomedicine and Health, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China. Electronic address: [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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.95 kDa 
• Atom Count: 2,534 
• Modeled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	312	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: ligA, EF_0722 EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837V6  Go to UniProtKB:  Q837V6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN (Subject of Investigation/LOI)	B [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.256 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.48	α = 90
b = 92.48	β = 90
c = 74.29	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MoRDa	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Chen, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2025-01-29
  Changes: Database references, Structure summary