1SZ1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.21 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.360 
  • R-Value Observed: 0.361 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1038/nature02711
  • Primary Citation of Related Structures:  
    1SZ1, 1TFY, 1TFW

  • 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 nucleotidyltransferase ...

    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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA nucleotidyltransferaseAB437Archaeoglobus fulgidusMutation(s): 0 
EC: 2.7.7.25 (PDB Primary Data), 2.7.7.72 (UniProt)
Find proteins for O28126 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28126 
Go to UniProtKB:  O28126
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
T-RNA (76-MER)E, F76N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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