tRNA processing enzyme (apo form 2)

Experimental Data Snapshot

  • Resolution: 4.00 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase

Yamashita, S.Takeshita, D.Tomita, K.

(2014) Structure 22: 315-325

  • DOI: https://doi.org/10.1016/j.str.2013.12.002
  • Primary Citation of Related Structures:  
    3WFO, 3WFP, 3WFQ, 3WFR, 3WFS

  • PubMed Abstract: 

    The 3'-terminal CCA (CCA-3' at positions 74-76) of tRNA is synthesized by CCA-adding enzyme using CTP and ATP as substrates, without a nucleic acid template. In Aquifex aeolicus, CC-adding and A-adding enzymes collaboratively synthesize the CCA-3'. The mechanism of CCA-3' synthesis by these two enzymes remained obscure. We now present crystal structures representing CC addition onto tRNA by A. aeolicus CC-adding enzyme. After C₇₄ addition in an enclosed active pocket and pyrophosphate release, the tRNA translocates and rotates relative to the enzyme, and C₇₅ addition occurs in the same active pocket as C₇₄ addition. At both the C₇₄-adding and C₇₅-adding stages, CTP is selected by Watson-Crick-like hydrogen bonds between the cytosine of CTP and conserved Asp and Arg residues in the pocket. After C₇₄C₇₅ addition and pyrophosphate release, the tRNA translocates further and drops off the enzyme, and the CC-adding enzyme terminates RNA polymerization.

  • Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly A polymerase
A, B, C, D, E
A, B, C, D, E, F, G, H
497Aquifex aeolicus VF5synthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: pcnB2
Find proteins for O67911 (Aquifex aeolicus (strain VF5))
Explore O67911 
Go to UniProtKB:  O67911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67911
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 4.00 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.91α = 90
b = 138.36β = 111.04
c = 147.62γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2017-06-28
    Changes: Source and taxonomy
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description