3OY6

The crystal structure of uPA complex with peptide inhibitor MH036 at pH4.6

Summary for 3OY6

• Entry DOI: 10.2210/pdb3oy6/pdb
• Related: 2NWN 3OX7 3OY5
• Descriptor: Urokinase-type plasminogen activator, MH036 (3 entities in total)
• Functional Keywords: urokinase-type plasminogen activator, peptidyl inhibitor, pharmacophore, hydrolase, 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: 30783.00

Authors

Jiang, L.G.,Andreasen, P.A.,Huang, M.D. (deposition date: 2010-09-22, release date: 2011-08-10, Last modification date: 2024-10-30)

Primary citation

Jiang, L.G.,Svane, A.S.P.,Sorensen, H.P.,Jensen, J.K.,Hosseini, M.,Chen, Z.,Weydert, C.,Nielsen, J.T.,Christensen, A.,Yuan, C.,Jensen, K.J.,Nielsen, N.C.,Malmendal, A.,Huang, M.D.,Andreasen, P.A.
The binding mechanism of a peptidic cyclic serine protease inhibitor
J.Mol.Biol., 412:235-250, 2011

PubMed Abstract: Serine proteases are classical objects for studies of catalytic and inhibitory mechanisms as well as interesting as therapeutic targets. Since small-molecule serine protease inhibitors generally suffer from specificity problems, peptidic inhibitors, isolated from phage-displayed peptide libraries, have attracted considerable attention. Here, we have investigated the mechanism of binding of peptidic inhibitors to serine protease targets. Our model is upain-1 (CSWRGLENHRMC), a disulfide-bond-constrained competitive inhibitor of human urokinase-type plasminogen activator with a noncanonical inhibitory mechanism and an unusually high specificity. Using a number of modified variants of upain-1, we characterised the upain-1-urokinase-type plasminogen activator complex using X-ray crystal structure analysis, determined a model of the peptide in solution by NMR spectroscopy, and analysed binding kinetics and thermodynamics by surface plasmon resonance and isothermal titration calorimetry. We found that upain-1 changes both main-chain conformation and side-chain orientations as it binds to the protease, in particular its Trp3 residue and the surrounding backbone. The properties of upain-1 are strongly influenced by the addition of three to four amino acids long N-terminal and C-terminal extensions to the core, disulfide-bond-constrained sequence: The C-terminal extension stabilises the solution structure compared to the core peptide alone, and the protease-bound structure of the peptide is stabilised by intrapeptide contacts between the N-terminal extension and the core peptide around Trp3. These results provide a uniquely detailed description of the binding of a peptidic protease inhibitor to its target and are of general importance in the development of peptidic inhibitors with high specificity and new inhibitory mechanisms.

PubMed: 21802428
DOI: 10.1016/j.jmb.2011.07.028

Experimental method

X-RAY DIFFRACTION (2.31 Å)