3H39

The complex structure of CCA-adding enzyme with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme

Toh, Y.Takeshita, D.Numata, T.Fukai, S.Nureki, O.Tomita, K.

(2009) EMBO J 28: 3353-3365

  • DOI: 10.1038/emboj.2009.260
  • Primary Citation of Related Structures:  
    3H37, 3H38, 3H39, 3H3A

  • PubMed Abstract: 
  • The CCA-adding enzyme synthesizes the CCA sequence at the 3' end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA-adding enzyme and its complexes with CTP or ATP were determined. The structure-based ...

    The CCA-adding enzyme synthesizes the CCA sequence at the 3' end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA-adding enzyme and its complexes with CTP or ATP were determined. The structure-based replacement of both the catalytic heads and nucleobase-interacting neck domains of the phylogenetically closely related Aquifex aeolicus A-adding enzyme by the corresponding domains of the T. maritima CCA-adding enzyme allowed the A-adding enzyme to add CCA in vivo and in vitro. However, the replacement of only the catalytic head domain did not allow the A-adding enzyme to add CCA, and the enzyme exhibited (A, C)-adding activity. We identified the region in the neck domain that prevents (A, C)-adding activity and defines the number of nucleotide incorporations and the specificity for correct CCA addition. We also identified the region in the head domain that defines the terminal A addition after CC addition. The results collectively suggest that, in the class II CCA-adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection.


    Organizational Affiliation

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba-shi, Ibaraki, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRNA nucleotidyl transferase-related proteinA, B441Thermotoga maritimaMutation(s): 0 
EC: 2.7.7.25
Find proteins for Q9WZH4 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9WZH4 
Go to UniProtKB:  Q9WZH4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.085α = 90
b = 64.07β = 100.88
c = 151.772γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-04-16 
  • Released Date: 2009-10-13 
  • Deposition Author(s): Toh, Y., Tomita, K.

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Database references