PDBsum entry 4jk5

Hydrolase/hydrolase inhibitor

PDB id: 4jk5

Contents

Protein chains

245 a.a.

18 a.a.

Ligands

SO4 ×4

P6G

ZBR

Metals

_CL ×2

Waters ×104

PDB id:

4jk5

Name:

Hydrolase/hydrolase inhibitor

Title:

Human urokinase-type plasminogen activator (upa) in complex with a bicyclic peptide inhibitor (uk18-d-ser)

Structure:

Urokinase-type plasminogen activator. Chain: a. Fragment: catalytic domain. Synonym: u-plasminogen activator, upa, urokinase-type plasminogen activator long chain a, urokinase-type plasminogen activator short chain a, urokinase-type plasminogen activator chain b. Engineered: yes. Mutation: yes. Bicyclic peptide uk18-d-ser, upa inhibitor.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: 9606. Gene: plau. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek-293. Synthetic: yes.

Resolution:

1.55Å R-factor: 0.146 R-free: 0.213

Authors:

S.A.Buth,P.G.Leiman,S.Chen,C.Heinis

Key ref:

S.Chen et al. (2013). Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids. Chembiochem, 14, 1316-1322. PubMed id: 23828687 DOI: 10.1002/cbic.201300228

Date:

09-Mar-13 Release date: 17-Jul-13

Protein chain

P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator from Homo sapiens

Seq: 431 a.a.

Struc: 245 a.a.*

Protein chain

No UniProt id for this chain

Struc: 18 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.73 - u-plasminogen activator.
• Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

DOI no: 10.1002/cbic.201300228

Chembiochem 14:1316-1322 (2013)

PubMed id: 23828687

Improving binding affinity and stability of peptide ligands by substituting glycines with D-amino acids.

S.Chen, D.Gfeller, S.A.Buth, O.Michielin, P.G.Leiman, C.Heinis.

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.