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- PDB-10fa: E. coli tRNA guanine transgylcosylase -

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Basic information

Entry
Database: PDB / ID: 10fa
TitleE. coli tRNA guanine transgylcosylase
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / RNA modifying enzyme
Function / homology
Function and homology information


tRNA wobble guanine modification / tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA queuosine(34) biosynthetic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsHarjung, A. / Devaraj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141939 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Cryo-EM reveals that tRNA-transglycosylase can bind and act upon two tRNAs.
Authors: Alexander Harjung / Ember M Ruth / Mariusz Matyszewski / Jaehee Park / Caroline Knittel / Evan McCormack / Neal K Devaraj /
Abstract: Bacterial tRNA-guanine transglycosylases (TGT) are essential enzymes involved in tRNA modification, contributing to the virulence of multiple pathogens. TGT from was the first protein of this family ...Bacterial tRNA-guanine transglycosylases (TGT) are essential enzymes involved in tRNA modification, contributing to the virulence of multiple pathogens. TGT from was the first protein of this family to be isolated and purified, and as such has served as a model enzyme for the biochemical characterization of TGTs. TGT is also one of the most disease-relevant TGTs, sharing high sequence identity with TGTs from several human pathogenic bacteria, including spp. and spp. Notably, TGTs from some strains are sequence-identical to the enzyme. In addition, as a highly promiscuous enzyme, TGT has found use as an RNA-modification tool in chemical biology, enabling site-specific covalent RNA modification in vitro and in vivo. For these reasons, there has been significant interest in solving the structure of TGT. However, crystallization of TGT has proven difficult, and to date, structural insights have relied on surrogate TGT enzymes from other organisms. Here, we present the cryo-EM structure of TGT and its covalent intermediate with a full-length tRNA. Unexpectedly, the structure reveals that the TGT dimer binds and acts upon two tRNAs, which is unlike all other known TGTs. Closer analysis of the TGT-tRNA complex reveals several important interactions outside of the enzyme's active site, that facilitate RNA binding and stabilize the conformational change of the tRNA anticodon loop. Based on these structural insights, we were able to design improved, high-affinity, TGT substrate RNA hairpins.
History
DepositionJan 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
B: Queuine tRNA-ribosyltransferase
C: Queuine tRNA-ribosyltransferase
D: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,5808
Polymers178,3194
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 44579.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal STREP tag C-terminal His tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tgt, b0406, JW0396 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A847, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli TGT / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89837 / Symmetry type: POINT
RefinementHighest resolution: 3.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212208
ELECTRON MICROSCOPYf_angle_d0.47816456
ELECTRON MICROSCOPYf_dihedral_angle_d3.891660
ELECTRON MICROSCOPYf_chiral_restr0.041720
ELECTRON MICROSCOPYf_plane_restr0.0042172

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