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 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 

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
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*C)-3')B2N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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

Download SDF File 
Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 100.434α = 90.00
b = 100.434β = 90.00
c = 40.333γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

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