7NQ4

Human tRNA guanine transglycosylase (TGT), RNA-bound covalent intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional insights into human tRNA guanine transgylcosylase.

Sievers, K.Welp, L.Urlaub, H.Ficner, R.

(2021) RNA Biol 18: 382-396

  • DOI: https://doi.org/10.1080/15476286.2021.1950980
  • Primary Citation of Related Structures:  
    7NQ4

  • PubMed Abstract: 

    The eukaryotic tRNA guanine transglycosylase (TGT) is an RNA modifying enzyme incorporating queuine, a hypermodified guanine derivative, into the tRNAs Asp,Asn,His,Tyr . While both subunits of the functional heterodimer have been crystallized individually, much of our understanding of its dimer interface or recognition of a target RNA has been inferred from its more thoroughly studied bacterial homolog. However, since bacterial TGT, by incorporating queuine precursor preQ 1 , deviates not only in function, but as a homodimer, also in its subunit architecture, any inferences regarding the subunit association of the eukaryotic heterodimer or the significance of its unique catalytically inactive subunit are based on unstable footing. Here, we report the crystal structure of human TGT in its heterodimeric form and in complex with a 25-mer stem loop RNA, enabling detailed analysis of its dimer interface and interaction with a minimal substrate RNA. Based on a model of bound tRNA, we addressed a potential functional role of the catalytically inactive subunit QTRT2 by UV-crosslinking and mutagenesis experiments, identifying the two-stranded βEβF-sheet of the QTRT2 subunit as an additional RNA-binding motif.


  • Organizational Affiliation

    Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferase catalytic subunit 1405Homo sapiensMutation(s): 0 
Gene Names: QTRT1TGTTGUT
EC: 2.4.2.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXR0 (Homo sapiens)
Explore Q9BXR0 
Go to UniProtKB:  Q9BXR0
PHAROS:  Q9BXR0
GTEx:  ENSG00000213339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXR0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferase accessory subunit 2415Homo sapiensMutation(s): 0 
Gene Names: QTRT2QTRTD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H974 (Homo sapiens)
Explore Q9H974 
Go to UniProtKB:  Q9H974
PHAROS:  Q9H974
GTEx:  ENSG00000151576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H974
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.84α = 90
b = 56.96β = 124.935
c = 102.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2021-12-29
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description