Molecular basis for the interaction between human choline kinase alpha and the SH3 domain of the c-Src tyrosine kinase

Abstract

Choline kinase alpha is a 457-residue protein that catalyzes the reaction between ATP and choline to yield ADP and phosphocholine. This metabolic action has been well studied because of choline kinase’s link to cancer malignancy and poor patient prognosis. As the myriad of x-ray crystal structures available for this enzyme show, chemotherapeutic drug design has centered on stopping the catalytic activity of choline kinase and reducing the downstream metabolites it produces. Furthermore, these crystal structures only reveal the catalytic domain of the protein, residues 80–457. However, recent studies provide evidence for a non-catalytic protein-binding role for choline kinase alpha. Here, we show that choline kinase alpha interacts with the SH3 domain of c-Src. Co-precipitation assays, surface plasmon resonance, and crystallographic analysis of a 1.5 Å structure demonstrate that this interaction is specific and is mediated by the poly-proline region found N-terminal to the catalytic domain of choline kinase. Taken together, these data offer strong evidence that choline kinase alpha has a heretofore underappreciated role in protein-protein interactions, which offers an exciting new way to approach drug development against this cancer-enhancing protein.

Recent advances in the design of choline kinase α inhibitors and the molecular basis of their inhibition

“…Kall et al have also very recently demonstrated, through SPR and crystallographic analysis, that ChoKα interacts with cSrc by a non-catalytic poly-proline motif (residues 60-69; see PDB ID: 6C4S) located in hChoKα N-terminal domain. 83 This finding could lead to the design of new inhibitors that disrupt this hChoKα-cSrc interaction.…”

DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks

“…ChoKα catalyzes the phosphorylation of choline to phosphocholine, and its high expression has proven to be associated with cancer malignancy and poor patient prognosis ( Ramírez De Molina et al , 2002 , 2005 ). Recent biophysical and biochemical studies ( Kall et al , 2019 ) have demonstrated that the ChoKα poly-proline region in residues 49–79 (especially prolines 61 and 62) mediates the physical interaction between ChoKα and the SH3 domain of c-Src tyrosine kinases. It can be seen in the ChoKα importance map ( Fig.…”

“…( b ) Analysis of the potential importance of each residue in ChoKα for interaction with the SH3 domain of c-Src. The poly-proline region in ChoKα residues 53–78 harbors relatively higher scores in the importance map , which are reported crucial for the interaction with the SH3 domain of c-Src ( Kall et al , 2019 )…”

Choline Kinase: An Unexpected Journey for a Precision Medicine Strategy in Human Diseases

“…Phosphorylation of ChoKα seems to correlate with a higher cell proliferation rate. Recently, this interaction has been mapped at the SH3 domain of c-Src and the poly-proline region N-terminal of ChoKα [99]. The relationship of ChoKα and EGFR, has also been reported in lung [100] and liver tumors [35] and has been associated with resistance to EGFR inhibitors [35].…”