9LD3 | pdb_00009ld3

The complex structure of K63A/2',3',5'-P-A/ADPR

• PDB DOI: https://doi.org/10.2210/pdb9LD3/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-01-05 Released: 2025-11-12 
• Deposition Author(s): Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Crystal structures and snapshots along Tpt1-catalyzed phosphate transfer from nucleic acid to NAD.

Cao, C., Yang, J., Zhang, W., Chen, J., Gao, Y., Yao, Y., Zhang, Y., Li, H., Li, L., Luo, Z., Wang, C., Tang, G., Cui, R., Liu, H., Wang, Q., Huang, Z., Ma, J., Gan, J.

(2025) Nat Commun 16: 10888-10888

• PubMed: 41345401 
• DOI: https://doi.org/10.1038/s41467-025-65881-y
• Primary Citation Related Structures: 
  9LD3, 9LD4, 9LD6, 9LDA, 9LDC, 9LDD, 9LDE, 9LDF, 9LDG, 9LDH, 9LDI


• PubMed Abstract: 
  

  Tpt1/TRPT1/KptA family proteins are evolutionarily conserved in all three domains of life. In fungi and plants, Tpt1 transfers 2'-PO ₄ ^2- from tRNA splice junction to NAD ⁺ , which is the final step of tRNA maturation and is critical for the function of tRNA. In mammals and bacteria, Tpt1-catalyzed reaction leads to 5'-end ADP ribosylation, a reversible chemical modification of nucleic acids. Based on in vivo and in vitro biochemical studies, a two-step catalytic mechanism has been established for Tpt1-catalyzed RNA 2'-PO ₄ ^2- transfer, including (i) the 2'-PO ₄ ^2- attacks NAD ⁺ , releasing nicotinamide and forming a 2'-phospho-ADP-ribosylated RNA (2'-p-ADPR-RNA) intermediate; and (ii) transesterification of the ADP-ribose 2"-OH to RNA 2'-PO ₄ ^2- , displacing the 2'-OH RNA and producing ADP-ribose-1",2"-cyclic phosphate (Appr>P). However, neither 2'-p-ADPR-RNA intermediate nor Appr>P product has been captured in any reported Tpt1 structures. Here, we report a series of crystal structures of T. kodakarensis Tpt1 (TkoTpt1), capturing the key 2'-p-ADPR-RNA intermediate. In addition, our structures also capture the 5'-p-ADPR-DNA intermediate and Appr>P product. Structural analysis and in vitro catalytic assays revealed that TkoTpt1 utilizes similar mechanism in 2'-PO ₄ ^2- and 5'-PO ₄ ^2- transfer. In conclusion, our structures reaffirm the catalytic mechanism of Tpt1-catalyzed phosphate transfer.

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Organizational Affiliation: 
• State Key Laboratory of Genetics and Development of Complex Phenotypes, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University school of Medicine, Shanghai, China.
Szostak Large Nucleic Acids Institute and SeNA Research Institute, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
State Key Laboratory of Genetics and Development of Complex Phenotypes, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.16 kDa 
• Atom Count: 3,267 
• Modeled Residue Count: 358 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA 2'-phosphotransferase	A, B	180	Thermococcus kodakarensis KOD1	Mutation(s): 1  Gene Names: kptA, TK0302 EC: 2.7.1
UniProt
Find proteins for Q5JFX3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFX3  Go to UniProtKB:  Q5JFX3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	D [auth A], H [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
A1EJC (Subject of Investigation/LOI)	E [auth A], G [auth B]	[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-diphosphonooxy-oxolan-2-yl]methyl dihydrogen phosphate C10 H16 N5 O13 P3 JRIZSBGDMDSKRF-KQYNXXCUSA-N
GOL	C [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.647	α = 90
b = 87.862	β = 90
c = 65.528	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Database references