1VFG

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.286 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4WC2


Literature

Structural basis for template-independent RNA polymerization.

Tomita, K.Fukai, S.Ishitani, R.Ueda, T.Takeuchi, N.Vassylyev, D.G.Nureki, O.

(2004) Nature 430: 700-704

  • DOI: https://doi.org/10.1038/nature02712
  • Primary Citation of Related Structures:  
    1VFG

  • PubMed Abstract: 

    The 3'-terminal CCA nucleotide sequence (positions 74-76) of transfer RNA is essential for amino acid attachment and interaction with the ribosome during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, 'CCA-adding enzyme', using CTP and ATP as substrates. Despite structural and biochemical studies, the mechanism by which the CCA-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. Here we present the crystal structure of Aquifex aeolicus CCA-adding enzyme, bound to a primer tRNA lacking the terminal adenosine and an incoming ATP analogue, at 2.8 A resolution. The enzyme enfolds the acceptor T helix of the tRNA molecule. In the catalytic pocket, C75 is adjacent to ATP, and their base moieties are stacked. The complementary pocket for recognizing C74-C75 of tRNA forms a 'protein template' for the penultimate two nucleotides, mimicking the nucleotide template used by template-dependent polymerases. These results are supported by systematic analyses of mutants. Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization.


  • Organizational Affiliation

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaragi 305-8666, Japan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
poly A polymeraseC [auth A],
D [auth B]
390Aquifex aeolicusMutation(s): 0 
EC: 2.7.7.19 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for O66728 (Aquifex aeolicus (strain VF5))
Explore O66728 
Go to UniProtKB:  O66728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66728
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.476α = 90
b = 125.9β = 90
c = 58.92γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted APCClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations