PDBsum entry 5hgg

Hydrolase/inhibitor

PDB id: 5hgg

Contents

Protein chains

246 a.a.

128 a.a.

Ligands

GOL ×5

SO4 ×2

TWN ×3

MES

Waters ×287

PDB id:

5hgg

Name:

Hydrolase/inhibitor

Title:

Crystal structure of upa in complex with a camelid-derived antibody fragment

Structure:

Urokinase-type plasminogen activator. Chain: a, b. Fragment: unp residues 179-424. Synonym: upa. Engineered: yes. Mutation: yes. Camelid derived antibody fragment, nb4. Chain: s, t. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plau. Expressed in: komagataella pastoris cbs 7435. Expression_system_taxid: 981350. Vicugna pacos. Organism_taxid: 30538. Expressed in: escherichia coli.

Resolution:

1.97Å R-factor: 0.169 R-free: 0.196

Authors:

K.W.Y.Yung,T.Kromann-Hansen,P.A.Andreasen,J.C.K.Ngo

Key ref:

T.Kromann-Hansen et al. (2016). A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior. J Biol Chem, 291, 15156-15168. PubMed id: 27226628 DOI: 10.1074/jbc.M116.732503

Date:

08-Jan-16 Release date: 01-Jun-16

Protein chains

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

Seq: 431 a.a.

Struc: 246 a.a.*

Protein chains

No UniProt id for this chain

Struc: 128 a.a.

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

Enzyme reactions

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

DOI no: 10.1074/jbc.M116.732503

J Biol Chem 291:15156-15168 (2016)

PubMed id: 27226628

A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.

T.Kromann-Hansen, E.Oldenburg, K.W.Yung, G.H.Ghassabeh, S.Muyldermans, P.J.Declerck, M.Huang, P.A.Andreasen, J.C.Ngo.

ABSTRACT

A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30-40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors.