1J2B

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme

Ishitani, R.Nureki, O.Nameki, N.Okada, N.Nishimura, S.Yokoyama, S.

(2003) Cell 113: 383-394

  • DOI: 10.1016/s0092-8674(03)00280-0
  • Primary Citation of Related Structures:  
    1J2B

  • PubMed Abstract: 
  • Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotid ...

    Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Archaeosine tRNA-guanine transglycosylaseAB582Pyrococcus horikoshiiMutation(s): 0 
EC: 2.4.2.29 (PDB Primary Data), 2.4.2.48 (UniProt)
Find proteins for O58843 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58843 
Go to UniProtKB:  O58843
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
tRNA(Val)C, D77N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.834α = 90
b = 230.834β = 90
c = 269.255γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance