4OI2 image
Entry Detail
PDB ID:
4OI2
Title:
C. Elegans Clp1 and ADP and Mg2+ (turnover state)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-01-18
Release Date:
2014-05-14
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 31
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Protein clpf-1
Chain IDs:A
Chain Length:431
Number of Molecules:1
Biological Source:Caenorhabditis elegans
Primary Citation
RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Mol.Cell 54 975 986 (2014)
PMID: 24813946 DOI: 10.1016/j.molcel.2014.04.005

Abstact

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.

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Primary Citation of related structures