8TG5

tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with branched 2'-PO4 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.

Jacewicz, A.Dantuluri, S.Shuman, S.

(2023) Proc Natl Acad Sci U S A 120: e2312999120-e2312999120

  • DOI: https://doi.org/10.1073/pnas.2312999120
  • Primary Citation of Related Structures:  
    8TFI, 8TFX, 8TFY, 8TFZ, 8TG3, 8TG4, 8TG5, 8TG6

  • PubMed Abstract: 

    Tpt1 is an essential agent of fungal and plant tRNA splicing that removes an internal RNA 2'-phosphate generated by tRNA ligase. Tpt1 also removes the 2'-phosphouridine mark installed by Ark1 kinase in the V-loop of archaeal tRNAs. Tpt1 performs a two-step reaction in which the 2'-PO 4 attacks NAD + to form an RNA-2'-phospho-(ADP-ribose) intermediate, and transesterification of the ADP-ribose O2″ to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate. Here, we present structures of archaeal Tpt1 enzymes, captured as product complexes with ADP-ribose-1″-PO 4 , ADP-ribose-2″-PO 4 , and 2'-OH RNA, and as substrate complexes with 2',5'-ADP and NAD + , that illuminate 2'-PO 4 junction recognition and catalysis. We show that archaeal Tpt1 enzymes can use the 2'-PO 4 -containing metabolites NADP + and NADPH as substrates for 2'-PO 4 transfer to NAD + . A role in 2'-phospho-NADP(H) dynamics provides a rationale for the prevalence of Tpt1 in taxa that lack a capacity for internal RNA 2'-phosphorylation.


  • Organizational Affiliation

    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable RNA 2'-phosphotransferase177Pyrococcus horikoshii OT3Mutation(s): 1 
Gene Names: kptAPH0160
EC: 2.7.1
UniProt
Find proteins for O57899 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57899 
Go to UniProtKB:  O57899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57899
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9S2 (Subject of Investigation/LOI)
Query on 9S2

Download Ideal Coordinates CCD File 
B [auth A](2S,3R,4R,5S)-2-(6-amino-9H-purin-9-yl)-4-{[(S)-{[(2R,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-({[(S)-{[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)oxolan-3-yl dihydrogen phosphate (non-preferred name)
C30 H38 N15 O19 P3
QNZAOYRRZJFVRM-ZNIXMAFJSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.291α = 90
b = 45.344β = 90
c = 125.239γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM126945
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30-GM124165
Department of Energy (DOE, United States)United StatesDE-SC0012704
Other governmentUnited StatesHEI-S10OD021527

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Database references