PDBsum entry 2nwn

Hydrolase

PDB id: 2nwn

Contents

Protein chains

240 a.a. *

12 a.a. *

Waters ×133

* Residue conservation analysis

PDB id:

2nwn

Name:

Hydrolase

Title:

New pharmacophore for serine protease inhibition revealed by crystal structure of human urokinase-type plasminogen activator complexed with a cyclic peptidyl inhibitor, upain-1

Structure:

Plasminogen activator, urokinase. Chain: a. Fragment: c-terminal domain, residues 16-250. Synonym: upa. Engineered: yes. Mutation: yes. Upain-1. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Synthetic: yes. Other_details: this peptide was chemically synthesized by solid phase synthesis and purified by reverse phase hplc.

Resolution:

2.15Å R-factor: 0.218 R-free: 0.261

Authors:

G.Zhao,C.Yuan,T.Wind,P.A.Andreasen,Z.Huang,M.Huang,Structural Genomics Consortium (Sgc)

Key ref:

G.Zhao et al. (2007). Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1. J Struct Biol, 160, 1-10. PubMed id: 17692534

Date:

16-Nov-06 Release date: 16-Oct-07

Protein chain

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

Seq: 431 a.a.

Struc: 240 a.a.*

Protein chain

No UniProt id for this chain

Struc: 12 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.

J Struct Biol 160:1-10 (2007)

PubMed id: 17692534

Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1.

G.Zhao, C.Yuan, T.Wind, Z.Huang, P.A.Andreasen, M.Huang.

ABSTRACT

Urokinase-type plasminogen activator (uPA) plays a crucial role in the regulation of plasminogen activation, tumor cell adhesion and migration. The inhibition of uPA activity is a promising mechanism for anti-cancer therapy. A cyclic peptidyl inhibitor, upain-1, CSWRGLENHRMC, was identified recently as a competitive and highly specific uPA inhibitor. We determined the crystal structure of uPA in complex with upain-1 at 2.15 A. The structure reveals that the cyclic peptide adopts a rigid conformation stabilized by a disulfide bond (residues 1-12) and three tight beta turns (residues 3-6, 6-9, 9-12). The Glu7 residue of upain-1 forms hydrogen bonds with the main chain nitrogen atoms of residues 4, 5, and 6 of upain-1, and is also critical for maintaining the active conformation of upain-1. The Arg4 of upain-1 is inserted into the uPA's specific S1 pocket. The Ser2 residue of upain-1 locates close to the S1beta pocket of uPA. The Gly5 and Glu7 residues of upain-1 occupy the S2 pocket and the oxyanion hole of uPA, respectively. Furthermore, the Asn8 residue of upain-1 binds to the 37- and 60-loops of uPA and renders the specificity of upain-1 for uPA. Based on this structure, a new pharmacophore for the design of highly specific uPA inhibitors was proposed.