7CV1

Structure of human tRNAHis guanylyltransferase (Thg1) in the presence of human mitochondrial tRNAHis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Analysis of GTP addition in the reverse (3'-5') direction by human tRNA His guanylyltransferase.

Nakamura, A.Wang, D.Komatsu, Y.

(2021) RNA 27: 665-675

  • DOI: https://doi.org/10.1261/rna.078287.120
  • Primary Citation of Related Structures:  
    7CV1

  • PubMed Abstract: 

    Human tRNA His guanylyltransferase (HsThg1) catalyzes the 3'-5' addition of guanosine triphosphate (GTP) to the 5'-end (-1 position) of tRNA His , producing mature tRNA His In human cells, cytoplasmic and mitochondrial tRNA His have adenine (A) or cytidine (C), respectively, opposite to G -1 Little attention has been paid to the structural requirements of incoming GTP in 3'-5' nucleotidyl addition by HsThg1. In this study, we evaluated the incorporation efficiencies of various GTP analogs by HsThg1 and compared the reaction mechanism with that of Candida albicans Thg1 (CaThg1). HsThg1 incorporated GTP opposite A or C in the template most efficiently. In contrast to CaThg1, HsThg1 could incorporate UTP opposite A, and guanosine diphosphate (GDP) opposite C. These results suggest that HsThg1 could transfer not only GTP, but also other NTPs, by forming Watson-Crick (WC) hydrogen bonds between the incoming NTP and the template base. On the basis of the molecular mechanism, HsThg1 succeeded in labeling the 5'-end of tRNA His with biotinylated GTP. Structural analysis of HsThg1 was also performed in the presence of the mitochondrial tRNA His Structural comparison of HsThg1 with other Thg1 family enzymes suggested that the structural diversity of the carboxy-terminal domain of the Thg1 enzymes might be involved in the formation of WC base-pairing between the incoming GTP and template base. These findings provide new insights into an unidentified biological function of HsThg1 and also into the applicability of HsThg1 to the 5'-terminal modification of RNAs.


  • Organizational Affiliation

    Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable tRNA(His) guanylyltransferase
A, B, C, D
277Homo sapiensMutation(s): 0 
Gene Names: THG1LICF45
EC: 2.7.7.79
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWX6 (Homo sapiens)
Explore Q9NWX6 
Go to UniProtKB:  Q9NWX6
PHAROS:  Q9NWX6
GTEx:  ENSG00000113272 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWX6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.878α = 90
b = 155.878β = 90
c = 201.5γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16K18511
Japan Society for the Promotion of Science (JSPS)Japan19K06519

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description