PDBsum entry 5lhp

Hydrolase

PDB id: 5lhp

Contents

Protein chains

247 a.a.

135 a.a.

Ligands

SO4 ×14

EDO ×2

PBZ

Waters ×84

PDB id:

5lhp

Name:

Hydrolase

Title:

The p-aminobenzamidine active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody nb7

Structure:

Urokinase-type plasminogen activator. Chain: a. Synonym: upa. Engineered: yes. Mutation: yes. Camelid-derived antibody fragment. Chain: b. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: plau. Expressed in: escherichia coli. Expression_system_taxid: 562. Vicugna pacos. Organism_taxid: 30538. Expression_system_taxid: 562

Resolution:

2.63Å R-factor: 0.207 R-free: 0.228

Authors:

T.Kromann-Hansen,E.L.Lange,H.P.Sorensen,G.H.Ghassabeh,M.Huang, J.K.Jensen,S.Muyldermans,P.J.Declerck,P.A.Andreasen

Key ref:

T.Kromann-Hansen et al. (2017). Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep, 7, 3385. PubMed id: 28611361

Date:

12-Jul-16 Release date: 28-Jun-17

Protein chain

P06869  (UROK_MOUSE) -  Urokinase-type plasminogen activator from Mus musculus

Seq: 433 a.a.

Struc: 247 a.a.*

Protein chain

No UniProt id for this chain

Struc: 135 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.

Sci Rep 7:3385 (2017)

PubMed id: 28611361

Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator.

T.Kromann-Hansen, E.Louise Lange, H.Peter Sørensen, G.Hassanzadeh-Ghassabeh, M.Huang, J.K.Jensen, S.Muyldermans, P.J.Declerck, E.A.Komives, P.A.Andreasen.

ABSTRACT

Although trypsin-like serine proteases have flexible surface-exposed loops and are known to adopt higher and lower activity conformations, structural determinants for the different conformations have remained largely obscure. The trypsin-like serine protease, urokinase-type plasminogen activator (uPA), is central in tissue remodeling processes and also strongly implicated in tumor metastasis. We solved five X-ray crystal structures of murine uPA (muPA) in the absence and presence of allosteric molecules and/or substrate-like molecules. The structure of unbound muPA revealed an unsuspected non-chymotrypsin-like protease conformation in which two β-strands in the core of the protease domain undergoes a major antiparallel-to-parallel conformational transition. We next isolated two anti-muPA nanobodies; an active-site binding nanobody and an allosteric nanobody. Crystal structures of the muPA:nanobody complexes and hydrogen-deuterium exchange mass spectrometry revealed molecular insights about molecular factors controlling the antiparallel-to-parallel equilibrium in muPA. Together with muPA activity assays, the data provide valuable insights into regulatory mechanisms and conformational flexibility of uPA and trypsin-like serine proteases in general.