4OI4

Protein complex of Clp1 bound to ATP and Mg2+ with Pcf11deltaN454deltaC563 of S. cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
mRNA cleavage and polyadenylation factor CLP1 AC453Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CLP1YOR250C
EC: 2.7.1.78
Find proteins for Q08685 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08685 
Go to UniProtKB:  Q08685
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein PCF11 BDU115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PCF11YDR228CYD9934.13C
Find proteins for P39081 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39081 
Go to UniProtKB:  P39081
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.64α = 90
b = 95.77β = 90
c = 181.58γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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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: 2015-01-14
    Changes: Structure summary