4X4R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 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, C457Archaeoglobus 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
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
G70A tRNA minihelix ending in CCACCB, D37Homo sapiens
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*CP*G)-3')E [auth H]2Homo sapiens
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    APC
    Query on APC

    Download Ideal Coordinates CCD File 
    F [auth A], K [auth C]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
    C11 H18 N5 O12 P3
    CAWZRIXWFRFUQB-IOSLPCCCSA-N
     Ligand Interaction
    MES
    Query on MES

    Download Ideal Coordinates CCD File 
    H [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
    C6 H13 N O4 S
    SXGZJKUKBWWHRA-UHFFFAOYSA-N
     Ligand Interaction
    TAR
    Query on TAR

    Download Ideal Coordinates CCD File 
    N [auth C]D(-)-TARTARIC ACID
    C4 H6 O6
    FEWJPZIEWOKRBE-LWMBPPNESA-N
     Ligand Interaction
    PEG
    Query on PEG

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

    Download Ideal Coordinates CCD File 
    I [auth A], J [auth A], M [auth C]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    G [auth A], L [auth C]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.266 
    • R-Value Work: 0.209 
    • R-Value Observed: 0.212 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 111.1α = 90
    b = 217.368β = 90
    c = 58.562γ = 90
    Software Package:
    Software NamePurpose
    SCALEPACKdata scaling
    PDB_EXTRACTdata extraction
    PHASERphasing
    PHENIXrefinement

    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: 2015-02-25
      Changes: Derived calculations
    • Version 1.2: 2017-11-22
      Changes: Derived calculations, Refinement description, Source and taxonomy
    • Version 1.3: 2019-11-20
      Changes: Author supporting evidence