4JK5

Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser)

Summary for 4JK5

• Entry DOI: 10.2210/pdb4jk5/pdb
• Related: 3QN7 4GLY
• Related PRD ID: PRD_000926
• Descriptor: Urokinase-type plasminogen activator, bicyclic peptide UK18-D-Ser, uPA inhibitor, SULFATE ION, ... (7 entities in total)
• Functional Keywords: serine protease, chymotrypsin fold, urokinase-type plasminogen activator, bicyclic peptide inhibitor, d-amino acid, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Cellular location: Secreted: P00749
• Total number of polymer chains: 2
• Total formula weight: 30501.82

Authors

Buth, S.A.,Leiman, P.G.,Chen, S.,Heinis, C. (deposition date: 2013-03-09, release date: 2013-07-17, Last modification date: 2024-11-20)

Primary citation

Chen, S.,Gfeller, D.,Buth, S.A.,Michielin, O.,Leiman, P.G.,Heinis, C.
Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids.
Chembiochem, 14:1316-1322, 2013

PubMed Abstract: Improving the binding affinity and/or stability of peptide ligands often requires testing of large numbers of variants to identify beneficial mutations. Herein we propose a type of mutation that promises a high success rate. In a bicyclic peptide inhibitor of the cancer-related protease urokinase-type plasminogen activator (uPA), we observed a glycine residue that has a positive ϕ dihedral angle when bound to the target. We hypothesized that replacing it with a D-amino acid, which favors positive ϕ angles, could enhance the binding affinity and/or proteolytic resistance. Mutation of this specific glycine to D-serine in the bicyclic peptide indeed improved inhibitory activity (1.75-fold) and stability (fourfold). X-ray-structure analysis of the inhibitors in complex with uPA showed that the peptide backbone conformation was conserved. Analysis of known cyclic peptide ligands showed that glycine is one of the most frequent amino acids, and that glycines with positive ϕ angles are found in many protein-bound peptides. These results suggest that the glycine-to-D-amino acid mutagenesis strategy could be broadly applied.

PubMed: 23828687
DOI: 10.1002/cbic.201300228

Experimental method

X-RAY DIFFRACTION (1.55 Å)