4OHW

C. Elegans Clp1 bound to ATP, and Mn2+(ATP-bound state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 

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:  

  • 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 stru ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein clpf-1
A
431Caenorhabditis elegansMutation(s): 0 
Gene Names: clpf-1
Find proteins for P52874 (Caenorhabditis elegans)
Go to UniProtKB:  P52874
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
2PE
Query on 2PE

Download SDF File 
Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 99.340α = 90.00
b = 99.340β = 90.00
c = 40.800γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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