1TFW

How CCA is added to the 3' end of immature tRNA without the use of an oligonucleotide template


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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 nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template ...

    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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA nucleotidyltransferaseG [auth A], H [auth B], I [auth C], J [auth D]437Archaeoglobus fulgidusMutation(s): 0 
Gene Names: ccaAF2156
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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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'A [auth E]12N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-R(*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*CP*C)-3'E [auth G], B [auth H], D [auth I]13N/A
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-R(*GP*CP*GP*GP*AP*CP*CP*CP*GP*CP*AP*C)-3'C [auth F]12N/A
        Protein Feature View
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        • Reference Sequence
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        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          5'-R(*CP*GP*CP*GP*GP*AP*UP*CP*CP*GP*CP*AP*C)-3'F [auth J]13N/A
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          ATP
          Query on ATP

          Download Ideal Coordinates CCD File 
          L [auth B], N [auth D]ADENOSINE-5'-TRIPHOSPHATE
          C10 H16 N5 O13 P3
          ZKHQWZAMYRWXGA-KQYNXXCUSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          K [auth B], M [auth D]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.20 Å
          • R-Value Free: 0.242 
          • R-Value Work: 0.192 
          • R-Value Observed: 0.195 
          • Space Group: P 1 21 1
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 116.641α = 90
          b = 84.77β = 104.66
          c = 135.813γ = 90
          Software Package:
          Software NamePurpose
          REFMACrefinement
          HKL-2000data reduction
          SCALEPACKdata scaling
          AMoREphasing

          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: Advisory, Version format compliance