PKDCC L262R

The tyrosine-protein kinase PKDCC ("Protein Kinase Domain Containing, Cytoplasmic", but later discovered to be extracellular) is an extracellular protein that phosphorylates several matrix metalloprotease family members (MMP1, MMP13, MMP14, MMP19 and ERP29). The model shown is of a PKDCC dimer with ATP, magnesium ion and target peptide as a proxy for the larger target protein (see methods).

Residue 262 is a buried leucine 14Å away from the ATP and magnesium cofactors and packed with residues 279, 284 and 293, which are on a structural elements involved in binding these cofactors. The substitution to arginine (L262R) is predicted to result in a shift in position of nearby residues (e.g. L276 and L263) due to the introduction of a larger charged residue in a hydrophobic pocket, which would be expected to destablise the protein region. In fact, modelling predicts the variant to have a higher Gibbs free energy of folding relative to wild type (∆∆G), by 2.0 kcal/mol. This means that the variant may be less stable and has an altered the neighbourhood making likely to affect its functionality.

Methods

5 models of each monomeric PKDCC and dimeric PKDCC with and without a fragment of MMP1 were inferred using ColabFold run on a local cluster (University of Oxford, BioMedical Research Computing (BMRC)).

Due to the divergences of the targets of paralogue the binding mode of MMP1 could not be resolved as a consequence in the final model the target was taken from the crystal structure of pCDK2/cyclin A (PDB:1GY3) along with ATP and magnesium ion. The structure PDB:1GY3 contains ADP+NO3 as opposed to ATP, as a consequence these two molecules were converted into ATP using Fragmenstein.

Tyrosine kinases are generally dimers and modelling univocally suggested PKDCC forms a dimer by predicting the same interacting residues in all 5 models.

The difference in energy was first calculated with Venus using the EBI-AlphaFold2 model, then with PyRosetta on all 5 models generated by ColabFold.

peptide and nucleic acid chains

• 49-493:A
• 49-493:C
• 2-8:Y
• 2-8:Z

ligands

• ATP and :X
• MG and :X