Mechanism of CCA-adding enzymes specificity revealed by crystal structures of ternary complexes

Experimental Data Snapshot

  • Resolution: 6.21 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.360 
  • R-Value Observed: 0.361 

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Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.

Xiong, Y.Steitz, T.A.

(2004) Nature 430: 640-645

  • DOI: https://doi.org/10.1038/nature02711
  • Primary Citation of Related Structures:  
    1SZ1, 1TFW, 1TFY

  • PubMed Abstract: 

    Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. Here we describe the crystal structure of the Archaeoglobus fulgidus tRNA nucleotidyltransferase in complex with tRNA. We also present ternary complexes of this enzyme with both RNA duplex mimics of the tRNA acceptor stem that terminate with the nucleotides C74 or C75, as well as the appropriate incoming nucleoside 5'-triphosphates. A single nucleotide-binding pocket exists whose specificity for both CTP and ATP is determined by the protein side chain of Arg 224 and backbone phosphates of the tRNA, which are non-complementary to and thus exclude UTP and GTP. Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA.

  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry,Yale University, New Haven, Connecticut 06520, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA nucleotidyltransferaseC [auth A],
D [auth B]
437Archaeoglobus fulgidusMutation(s): 0 
Find proteins for O28126 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28126 
Go to UniProtKB:  O28126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28126
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
T-RNA (76-MER)A [auth E],
B [auth F]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 6.21 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.360 
  • R-Value Observed: 0.361 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.403α = 90
b = 218.403β = 90
c = 170.263γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description