4OHY

C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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 structures of Clp1 from Caenorhabditis elegans (ceClp1) in a number of nucleotide- and RNA-bound states along the reaction pathway ...

    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 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ANP
    Query on ANP

    Download Ideal Coordinates CCD File 
    A
    PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N
     Ligand Interaction
    2PE
    Query on 2PE

    Download Ideal Coordinates CCD File 
    A
    NONAETHYLENE GLYCOL
    C18 H38 O10
    YZUUTMGDONTGTN-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: 2.00 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.182 
    • R-Value Observed: 0.185 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 100.434α = 90
    b = 100.434β = 90
    c = 40.333γ = 120
    Software Package:
    Software NamePurpose
    XDSdata scaling
    REFMACrefinement
    XDSdata reduction
    XSCALEdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • 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