4OHW

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

Summary for 4OHW

• Entry DOI: 10.2210/pdb4ohw/pdb
• Related: 4OHV 4OHX 4OHY 4OHZ 4OI0 4OI1 4OI2
• Descriptor: Protein clpf-1, ADENOSINE-5'-TRIPHOSPHATE, MANGANESE (II) ION, ... (5 entities in total)
• Functional Keywords: polynucleotide kinase, rna binding protein
• Biological source: Caenorhabditis elegans (nematode)
• Cellular location: Nucleus : P52874
• Total number of polymer chains: 1
• Total formula weight: 48913.06

Authors

Dikfidan, A.,Loll, B.,Zeymer, C.,Clausen, T.,Meinhart, A. (deposition date: 2014-01-18, release date: 2014-05-14, Last modification date: 2024-02-28)

Primary citation

Dikfidan, A.,Loll, B.,Zeymer, C.,Magler, I.,Clausen, T.,Meinhart, A.
RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Mol.Cell, 54:975-986, 2014

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. 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.

PubMed: 24813946
DOI: 10.1016/j.molcel.2014.04.005

Experimental method

X-RAY DIFFRACTION (2.3 Å)