1Q2S

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Xie, W., Liu, X., Huang, R.H.

(2003) Nat.Struct.Mol.Biol. 10: 781-788

  • DOI: 10.1038/nsb976
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis T ...

    Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.

    Organizational Affiliation: 

    Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Queuine tRNA-ribosyltransferase
A, B, C, D
386Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)Mutation(s): 0 
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
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3'E20synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3')F20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
9DG
Query on 9DG
Download SDF File 
Download CCD File 
C
9-DEAZAGUANINE
C6 H6 N4 O
FFYPRJYSJODFFD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
N
Query on N
F
RNA LINKINGC5 H11 O7 P

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PQ1
Query on PQ1
E
RNA LINKINGC12 H18 N5 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 261.961α = 90.00
b = 261.961β = 90.00
c = 55.549γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-11-07
    Type: Data collection, Source and taxonomy