4X4T

Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme.

Kuhn, C.D.Wilusz, J.E.Zheng, Y.Beal, P.A.Joshua-Tor, L.

(2015) Cell 160: 644-658

  • DOI: 10.1016/j.cell.2015.01.005
  • Primary Citation of Related Structures:  
    4X4N, 4X4O, 4X4P, 4X4Q, 4X4R, 4X4S, 4X4T, 4X4U, 4X4V, 4X4W

  • PubMed Abstract: 
  • Transcription in eukaryotes produces a number of long noncoding RNAs (lncRNAs). Two of these, MALAT1 and Menβ, generate a tRNA-like small RNA in addition to the mature lncRNA. The stability of these tRNA-like small RNAs and bona fide tRNAs is monitored by the CCA-adding enzyme ...

    Transcription in eukaryotes produces a number of long noncoding RNAs (lncRNAs). Two of these, MALAT1 and Menβ, generate a tRNA-like small RNA in addition to the mature lncRNA. The stability of these tRNA-like small RNAs and bona fide tRNAs is monitored by the CCA-adding enzyme. Whereas CCA is added to stable tRNAs and tRNA-like transcripts, a second CCA repeat is added to certain unstable transcripts to initiate their degradation. Here, we characterize how these two scenarios are distinguished. Following the first CCA addition cycle, nucleotide binding to the active site triggers a clockwise screw motion, producing torque on the RNA. This ejects stable RNAs, whereas unstable RNAs are refolded while bound to the enzyme and subjected to a second CCA catalytic cycle. Intriguingly, with the CCA-adding enzyme acting as a molecular vise, the RNAs proofread themselves through differential responses to its interrogation between stable and unstable substrates.


    Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. Electronic address: leemor@cshl.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCA-adding enzymeA, C, E, F457Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: ccaAF_2156
EC: 2.7.7.72
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: 2
MoleculeChainsLengthOrganismImage
G70A tRNA minihelix ending in CCACCAB, D34Homo sapiens
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
G70A tRNA minihelix ending in CCACCAG31Homo sapiens
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(P*CP*G)-3')H2Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      RNA (5'-D(P*GP*G)-3')I2Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PEG
      Query on PEG

      Download Ideal Coordinates CCD File 
      M [auth E]DI(HYDROXYETHYL)ETHER
      C4 H10 O3
      MTHSVFCYNBDYFN-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      J [auth A], K [auth A], L [auth A]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.229 
      • R-Value Work: 0.186 
      • R-Value Observed: 0.188 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 115.422α = 90
      b = 83.959β = 103.51
      c = 135.32γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      PDB_EXTRACTdata extraction
      PHASERphasing
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Howard Hughes Medical Institute (HHMI)United States--

      Revision History  (Full details and data files)

      • Version 1.0: 2015-02-11
        Type: Initial release
      • Version 1.1: 2015-02-18
        Changes: Database references
      • Version 1.2: 2015-02-25
        Changes: Database references
      • Version 1.3: 2017-11-22
        Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
      • Version 1.4: 2019-11-20
        Changes: Author supporting evidence