4WC2

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: 
    0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

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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

This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1VFG


Literature

Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.

Yamashita, S.Martinez, A.Tomita, K.

(2015) Structure 23: 830-842

  • DOI: https://doi.org/10.1016/j.str.2015.03.013
  • Primary Citation of Related Structures:  
    4WBY, 4WBZ, 4WC0, 4WC1, 4WC2, 4WC3, 4WC4, 4WC5, 4WC6, 4WC7, 4X0A, 4X0B

  • PubMed Abstract: 

    The 3'-terminal CCA (C74C75A76-3') of tRNA is required for protein synthesis. In Aquifex aeolicus, the CCA-3' is synthesized by CC-adding and A-adding enzymes, although in most organisms, CCA is synthesized by a single CCA-adding enzyme. The mechanisms by which the A-adding enzyme adds only A76, but not C74C75, onto tRNA remained elusive. The complex structures of the enzyme with various tRNAs revealed the presence of a single tRNA binding site on the enzyme, with the enzyme measuring the acceptor-TΨC helix length of tRNA. The 3'-C75 of tRNA lacking A76 can reach the active site and the size and shape of the nucleotide binding pocket at the insertion stage are suitable for ATP. The 3'-C74 of tRNA lacking C75A76 cannot reach the active site, although CTP or ATP can bind the active pocket. Thus, the A-adding enzyme adds only A76, but not C74C75, onto tRNA.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly A polymerase396Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: pcnB1aq_411
EC: 2.7.7
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
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.92α = 90
b = 109.48β = 90
c = 125.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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 & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Refinement description