Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with ATP

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural basis of reverse nucleotide polymerization

Nakamura, A.Nemoto, T.Heinemann, I.U.Yamashita, K.Sonoda, T.Komoda, K.Tanaka, I.Soll, D.Yao, M.

(2013) Proc Natl Acad Sci U S A 110: 20970-20975

  • DOI: https://doi.org/10.1073/pnas.1321312111
  • Primary Citation of Related Structures:  
    3WBZ, 3WC0, 3WC1, 3WC2

  • PubMed Abstract: 

    Nucleotide polymerization proceeds in the forward (5'-3') direction. This tenet of the central dogma of molecular biology is found in diverse processes including transcription, reverse transcription, DNA replication, and even in lagging strand synthesis where reverse polymerization (3'-5') would present a "simpler" solution. Interestingly, reverse (3'-5') nucleotide addition is catalyzed by the tRNA maturation enzyme tRNA(His) guanylyltransferase, a structural homolog of canonical forward polymerases. We present a Candida albicans tRNA(His) guanylyltransferase-tRNA(His) complex structure that reveals the structural basis of reverse polymerization. The directionality of nucleotide polymerization is determined by the orientation of approach of the nucleotide substrate. The tRNA substrate enters the enzyme's active site from the opposite direction (180° flip) compared with similar nucleotide substrates of canonical 5'-3' polymerases, and the finger domains are on opposing sides of the core palm domain. Structural, biochemical, and phylogenetic data indicate that reverse polymerization appeared early in evolution and resembles a mirror image of the forward process.

  • Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Likely histidyl tRNA-specific guanylyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
271Candida albicans SC5314Mutation(s): 0 
Gene Names: CaO19.7063CAWG_05412orf19.7063THG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
HA [auth F]
I [auth A]
IA [auth F]
CA [auth E],
DA [auth E],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
MA [auth G],
N [auth B],
NA [auth G],
O [auth B],
RA [auth H],
S [auth C],
SA [auth H],
T [auth C],
X [auth D],
Y [auth D]
C10 H16 N5 O13 P3
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
EA [auth E]
FA [auth E]
GA [auth E]
AA [auth D],
BA [auth D],
EA [auth E],
FA [auth E],
GA [auth E],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
QA [auth G],
R [auth B],
TA [auth H],
U [auth C],
UA [auth H],
V [auth C],
VA [auth H],
W [auth C],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.83α = 90
b = 217.87β = 113.68
c = 87.24γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
BSSdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Other
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description