4OI0

bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.

Dikfidan, A.Loll, B.Zeymer, C.Magler, I.Clausen, T.Meinhart, A.

(2014) Mol Cell 54: 975-986

  • DOI: 10.1016/j.molcel.2014.04.005
  • Primary Citation of Related Structures:  
    4OHV, 4OHW, 4OHX, 4OHY, 4OHZ, 4OI0, 4OI1, 4OI2, 4OI4

  • PubMed Abstract: 
  • RNA-specific polynucleotide kinases of the Clp1 subfamily are key components of various RNA maturation pathways. However, the structural basis explaining their substrate specificity and the enzymatic mechanism is elusive. Here, we report crystal structur ...

    RNA-specific polynucleotide kinases of the Clp1 subfamily are key components of various RNA maturation pathways. However, the structural basis explaining their substrate specificity and the enzymatic mechanism is elusive. Here, we report crystal structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway. The combined structural and biochemical analysis of ceClp1 elucidates the RNA specificity and lets us derive a general model for enzyme catalysis of RNA-specific polynucleotide kinases. We identified an RNA binding motif referred to as "clasp" as well as a conformational switch that involves the essential Walker A lysine (Lys127) and regulates the enzymatic activity of ceClp1. Structural comparison with other P loop proteins, such as kinases, adenosine triphosphatases (ATPases), and guanosine triphosphatases (GTPases), suggests that the observed conformational switch of the Walker A lysine is a broadly relevant mechanistic feature.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg 69120, Germany. Electronic address: anton.meinhart@mpimf-heidelberg.mpg.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein clpf-1 A431Caenorhabditis elegansMutation(s): 0 
Gene Names: clpf-1F59A2.4
Find proteins for P52874 (Caenorhabditis elegans)
Explore P52874 
Go to UniProtKB:  P52874
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*C)-3')B2N/A
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    A
    ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    2PE
    Query on 2PE

    Download Ideal Coordinates CCD File 
    A
    NONAETHYLENE GLYCOL
    C18 H38 O10
    YZUUTMGDONTGTN-UHFFFAOYSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    A
    TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    SAR
    Query on SAR

    Download Ideal Coordinates CCD File 
    A
    SARCOSINE
    C3 H7 N O2
    FSYKKLYZXJSNPZ-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.280 
    • R-Value Work: 0.227 
    • R-Value Observed: 0.229 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 100.71α = 90
    b = 100.71β = 90
    c = 40.4γ = 120
    Software Package:
    Software NamePurpose
    MAR345dtbdata collection
    REFMACrefinement
    XDSdata reduction
    XSCALEdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-05-14
      Type: Initial release
    • Version 1.1: 2014-07-02
      Changes: Database references
    • Version 1.2: 2015-01-21
      Changes: Structure summary
    • Version 1.3: 2017-11-22
      Changes: Refinement description