3OTB | pdb_00003otb

Crystal structure of human tRNAHis guanylyltransferase (Thg1) - dGTP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.301 (Depositor), 0.304 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.255 (DCC) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

tRNAHis guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases.

Hyde, S.J.Eckenroth, B.E.Smith, B.A.Eberley, W.A.Heintz, N.H.Jackman, J.E.Doublie, S.

(2010) Proc Natl Acad Sci U S A 107: 20305-20310

  • DOI: https://doi.org/10.1073/pnas.1010436107
  • Primary Citation Related Structures: 
    3OTB, 3OTC, 3OTD, 3OTE

  • PubMed Abstract: 

    All known DNA and RNA polymerases catalyze the formation of phosphodiester bonds in a 5' to 3' direction, suggesting this property is a fundamental feature of maintaining and dispersing genetic information. The tRNA(His) guanylyltransferase (Thg1) is a member of a unique enzyme family whose members catalyze an unprecedented reaction in biology: 3'-5' addition of nucleotides to nucleic acid substrates. The 2.3-Å crystal structure of human THG1 (hTHG1) reported here shows that, despite the lack of sequence similarity, hTHG1 shares unexpected structural homology with canonical 5'-3' DNA polymerases and adenylyl/guanylyl cyclases, two enzyme families known to use a two-metal-ion mechanism for catalysis. The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases.


  • Organizational Affiliation
    • Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.

Macromolecule Content 

  • Total Structure Weight: 64.93 kDa 
  • Atom Count: 4,044 
  • Modeled Residue Count: 474 
  • Deposited Residue Count: 538 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
tRNA(His) guanylyltransferase
A, B
269Homo sapiensMutation(s): 0 
Gene Names: ICF45THG1L
EC: 2.7.7 (PDB Primary Data), 2.7.7.79 (UniProt)
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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT

Query on DGT



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
3PO

Query on 3PO



Download:Ideal Coordinates CCD File
G [auth A],
H [auth B]
TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.301 (Depositor), 0.304 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.255 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.912α = 90
b = 140.912β = 90
c = 81.227γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-09
    Changes: Source and taxonomy
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations