1PUD

TRNA-GUANINE TRANSGLYCOSYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange.

Romier, C.Reuter, K.Suck, D.Ficner, R.

(1996) EMBO J. 15: 2850-2857


  • PubMed Abstract: 
  • tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryo ...

    tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R-factor of 19% at 1.85 angstrom resolution. The structure consists of an irregular (beta/alpha)8-barrel with a tightly attached C-terminal zinc-containing subdomain. The packing of the subdomain against the barrel is mediated by an alpha-helix, located close to the C-terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ1 suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U33G34U35 sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA-enzyme intermediate. This structure is the first example of a (beta/alpha)-barrel protein interacting specifically with a nucleic acid.


    Related Citations: 
    • Purification, Crystallization, and Preliminary X-Ray Diffraction Studies of tRNA-Guanine Transglycosylase from Zymomonas Mobilis
      Romier, C.,Ficner, R.,Reuter, K.,Suck, D.
      (1996) Proteins 24: 516
    • Sequence Analysis and Overexpression of the Zymomonas Mobilis Tgt Gene Encoding tRNA-Guanine Transglycosylase: Purification and Biochemical Characterization of the Enzyme
      Reuter, K.,Ficner, R.
      (1995) J.Bacteriol. 177: 5284


    Organizational Affiliation

    European Molecular Biology Laboratory, Structural Biology Programme, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRNA-GUANINE TRANSGLYCOSYLASE
A
386Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)Gene Names: tgt
EC: 2.4.2.29
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Go to UniProtKB:  P28720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.100α = 90.00
b = 65.100β = 97.50
c = 71.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance