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- PDB-8omr: Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp -

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Basic information

Entry
Database: PDB / ID: 8omr
TitleHuman tRNA guanine transglycosylase (TGT) bound to tRNAAsp
Components
  • Queuine tRNA-ribosyltransferase accessory subunit 2
  • Queuine tRNA-ribosyltransferase catalytic subunit 1
  • tRNAAsp
KeywordsRNA BINDING PROTEIN / RNA modification / transglycosylation / nucleid acid-protein complex / tRNA binding
Function / homology
Function and homology information


tRNA-guanine transglycosylase complex / tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity ...tRNA-guanine transglycosylase complex / tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / mitochondrion / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Queuine tRNA-ribosyltransferase accessory subunit QTRTD1 / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
9-DEAZAGUANINE / RNA / RNA (> 10) / Queuine tRNA-ribosyltransferase catalytic subunit 1 / Queuine tRNA-ribosyltransferase accessory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSievers, K. / Neumann, P. / Susac, L. / Trowitzsch, S. / Tampe, R. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Structure / Year: 2024
Title: Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase.
Authors: Katharina Sievers / Piotr Neumann / Lukas Sušac / Stefano Da Vela / Melissa Graewert / Simon Trowitzsch / Dmitri Svergun / Robert Tampé / Ralf Ficner /
Abstract: Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine ...Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: tRNAAsp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4576
Polymers115,1763
Non-polymers2813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, assembly was verified by SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7200 Å2
ΔGint-38 kcal/mol
Surface area43440 Å2
MethodPISA

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Components

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


Mass: 44251.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zn ion and 9DG are ligands / Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT1, TGT, TGUT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BXR0, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1


Mass: 46775.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zn is an ion / Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT2, QTRTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H974
#3: RNA chain tRNAAsp


Mass: 24148.312 Da / Num. of mol.: 1 / Mutation: U1A, C2G, C3G, G69C, G70C, A71U / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-9DG / 9-DEAZAGUANINE


Mass: 150.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 44.46 sec. / Electron dose: 62.1 e/Å2 / Film or detector model: OTHER
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 463140 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037837
ELECTRON MICROSCOPYf_angle_d0.68210955
ELECTRON MICROSCOPYf_dihedral_angle_d11.8671700
ELECTRON MICROSCOPYf_chiral_restr0.0381295
ELECTRON MICROSCOPYf_plane_restr0.0051135

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