6EDE | pdb_00006ede

tRNA 2'-phosphotransferase

• PDB DOI: https://doi.org/10.2210/pdb6EDE/pdb

• Classification: TRANSFERASE
• Organism(s): Acetivibrio thermocellus ATCC 27405
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2018-08-09 Released: 2019-03-20 
• Deposition Author(s): Shuman, S., Goldgur, Y., Banerjee, 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: 1.55 Å
• R-Value Free: 
  0.188 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.

Banerjee, A., Munir, A., Abdullahu, L., Damha, M.J., Goldgur, Y., Shuman, S.

(2019) Nat Commun 10: 218-218

• PubMed: 30644400 
• DOI: https://doi.org/10.1038/s41467-018-08211-9
• Primary Citation Related Structures: 
  6E3A, 6EDE


• PubMed Abstract: 
  

  Tpt1 is an essential agent of fungal tRNA splicing that removes the 2'-PO ₄ at the splice junction generated by fungal tRNA ligase. Tpt1 catalyzes a unique two-step reaction whereby the 2'-PO ₄ attacks NAD ⁺ to form an RNA-2'-phospho-ADP-ribosyl intermediate that undergoes transesterification to yield 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate products. Because Tpt1 is inessential in exemplary bacterial and mammalian taxa, Tpt1 is seen as an attractive antifungal target. Here we report a 1.4 Å crystal structure of Tpt1 in a product-mimetic complex with ADP-ribose-1″-phosphate in the NAD ⁺ site and pAp in the RNA site. The structure reveals how Tpt1 recognizes a 2'-PO ₄ RNA splice junction and the mechanism of RNA phospho-ADP-ribosylation. This study also provides evidence that a bacterium has an endogenous phosphorylated substrate with which Tpt1 reacts.

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Organizational Affiliation: 
• Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, NY, 10065, USA.
Chemistry Department, McGill University, Montreal, Quebec, H3A0B8, Canada.
Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, NY, 10065, 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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.08 kDa 
• Atom Count: 1,700 
• Modeled Residue Count: 178 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA 2'-phosphotransferase	A	203	Acetivibrio thermocellus ATCC 27405	Mutation(s): 1  Gene Names: kptA, Cthe_3059 EC: 2.7.1
UniProt
Find proteins for A3DJX6 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DJX6  Go to UniProtKB:  A3DJX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HQG	B [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate C15 H24 N5 O17 P3 CUNFRFHBHMFVPH-KEOHHSTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.188 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.284	α = 90
b = 53.284	β = 90
c = 308.393	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Shuman, S., Goldgur, Y., Banerjee, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 GM126945

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description