8PBA

Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo)

Summary for 8PBA

• Entry DOI: 10.2210/pdb8pba/pdb
• EMDB information: 17582
• Descriptor: Dipeptidyl Peptidase Four (IV) family (1 entity in total)
• Functional Keywords: dipeptidylpeptidase, hydrolase
• Biological source: Caenorhabditis elegans
• Total number of polymer chains: 2
• Total formula weight: 212925.62

Authors

Gudipati, R.K.,Cavadini, S.,Kempf, G.,Grosshans, H. (deposition date: 2023-06-08, release date: 2024-06-26, Last modification date: 2025-01-15)

Primary citation

Gudipati, R.K.,Gaidatzis, D.,Seebacher, J.,Muehlhaeusser, S.,Kempf, G.,Cavadini, S.,Hess, D.,Soneson, C.,Grosshans, H.
Deep quantification of substrate turnover defines protease subsite cooperativity.
Mol.Syst.Biol., 20:1303-1328, 2024

PubMed Abstract: Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to a small number of events. Here, we develop qPISA (quantitative Protease specificity Inference from Substrate Analysis) to study Dipeptidyl Peptidase Four (DPP4), a key regulator of blood glucose levels. We use mass spectrometry to quantify >40,000 peptides from a complex, commercially available peptide mixture. By analyzing changes in substrate levels quantitatively instead of focusing on qualitative product identification through a binary classifier, we can reveal cooperative interactions within DPP4's active pocket and derive a sequence motif that predicts activity quantitatively. qPISA distinguishes DPP4 from the related C. elegans DPF-3 (a DPP8/9-orthologue), and we relate the differences to the structural features of the two enzymes. We demonstrate that qPISA can direct protein engineering efforts like the stabilization of GLP-1, a key DPP4 substrate used in the treatment of diabetes and obesity. Thus, qPISA offers a versatile approach for profiling protease and especially exopeptidase specificity, facilitating insight into enzyme mechanisms and biotechnological and clinical applications.

PubMed: 39468329
DOI: 10.1038/s44320-024-00071-4

Experimental method

ELECTRON MICROSCOPY (2.64 Å)