3WBZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.392 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.USA 110: 20970-20975

  • DOI: 10.1073/pnas.1321312111
  • Primary Citation of Related Structures:  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 synthe ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Likely histidyl tRNA-specific guanylyltransferase
A, B, C, D, E, F, G, H
271N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.392 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.830α = 90.00
b = 217.870β = 113.68
c = 87.240γ = 90.00
Software Package:
Software NamePurpose
BSSdata collection
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Other