6E3A

tRNA 2'-phosphotransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/s41467-018-08211-9
  • Primary Citation of 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.

    • Organizational Affiliation: 

    Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, NY, 10065, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable RNA 2'-phosphotransferase182Acetivibrio thermocellus ATCC 27405Mutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DJX6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA
Download Ideal Coordinates CCD File 
B [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
HQG
Query on HQG
Download Ideal Coordinates CCD File 
C [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: 1.40 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.367α = 90
b = 53.367β = 90
c = 308.903γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Omodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35 GM126945

Revision History  (Full details and data files)

  • 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