4X4N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CCA-adding enzymeA, D [auth C], F [auth E], G [auth F]457Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: ccaAF_2156
EC: 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
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
G70A tRNA minihelixC [auth B], E [auth D], B [auth G]32Homo sapiens
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(P*CP*G)-3')H [auth I]2Homo sapiens
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    5GP
    Query on 5GP

    Download Ideal Coordinates CCD File 
    K [auth B]GUANOSINE-5'-MONOPHOSPHATE
    C10 H14 N5 O8 P
    RQFCJASXJCIDSX-UUOKFMHZSA-N
     Ligand Interaction
    GMP
    Query on GMP

    Download Ideal Coordinates CCD File 
    J [auth B]GUANOSINE
    C10 H13 N5 O5
    NYHBQMYGNKIUIF-UUOKFMHZSA-N
     Ligand Interaction
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    I [auth A], L [auth C], N [auth E], O [auth F]SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    M [auth D]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.95 Å
    • R-Value Free: 0.249 
    • R-Value Work: 0.191 
    • R-Value Observed: 0.194 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 115.416α = 90
    b = 84.688β = 103.14
    c = 135.565γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    PDB_EXTRACTdata extraction
    PHASERphasing
    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