1Q2R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 

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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 Biol 10: 781-788

  • DOI: 10.1038/nsb976
  • Primary Citation of Related Structures:  
    1Q2R, 1Q2S

  • 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 TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferaseC [auth A], D [auth B], E [auth C], F [auth D]386Zymomonas mobilisMutation(s): 0 
Gene Names: tgt
EC: 2.4.2.29
UniProt
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore P28720 
Go to UniProtKB:  P28720
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    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')A [auth E], B [auth F]20synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.230 
    • R-Value Work: 0.181 
    • Space Group: I 4
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 264.856α = 90
    b = 264.856β = 90
    c = 55.911γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    AMoREphasing
    CNSrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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