5HC9

Thermotoga maritima CCA-adding enzyme complexed with tRNA_CCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of 3'-Matured tRNA Discrimination from 3'-Immature tRNA by Class-II CCA-Adding Enzyme

Yamashita, S.Tomita, K.

(2016) Structure 24: 918-925

  • DOI: https://doi.org/10.1016/j.str.2016.03.022
  • Primary Citation of Related Structures:  
    5HC9

  • PubMed Abstract: 

    CCA-adding enzyme adds the 3'-CCA of tRNA, using CTP and ATP as substrates, and terminates RNA synthesis after completion of CCA addition, without using a nucleic acid template. The complex structure of class-II Thermotoga maritima CCA-adding enzyme and mature tRNA with 3'-CCA revealed the mechanisms by which the enzyme terminates RNA synthesis after completion of 3'-CCA addition, and discriminates 3'-mature tRNA from 3'-immature tRNA. After completion of 3'-CCA addition at the catalytic site, the 3'-CCA refolds and relocates to the release site, which is discrete from the catalytic site. The 3'-CCA forms a continuously stacked, stable conformation together with the enzyme. Consequently, the 3'-mature tRNA rotates relative to the surface of the enzyme, and only the 3'-mature tRNA is ready for release. The 3'-regions of immature tRNAs cannot form the stable stacking conformation in the release site; thus, the 3' end is relocated in the catalytic site, and the 3'-CCA is reconstructed.


  • Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA nucleotidyl transferase-related protein
A, B
441Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_0715Tmari_0715
EC: 2.7.7.72
UniProt
Find proteins for Q9WZH4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZH4 
Go to UniProtKB:  Q9WZH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZH4
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
tRNAphe
C, D
76Thermotoga maritima
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.18α = 90
b = 96.19β = 110.3
c = 108.58γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology Agency (JST)JapanLS135

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description