PDBsum entry 4dte

Hydrolase inhibitor

PDB id: 4dte

Contents

Protein chains

374 a.a.

Ligands

NAG ×2

Waters ×443

PDB id:

4dte

Name:

Hydrolase inhibitor

Title:

Crystal structure of zebrafish plasminogen activator inhibitor-1 (pai- 1)

Structure:

Serpin peptidase inhibitor, clade e (nexin, plasminogen activator inhibitor type 1), member 1. Chain: a, b. Engineered: yes

Source:

Danio rerio. Leopard danio,zebra danio,zebra fish. Organism_taxid: 7955. Gene: serpine1. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: human embryonic kidney cells (hek-293).

Resolution:

1.96Å R-factor: 0.175 R-free: 0.219

Authors:

J.S.Johansen

Key ref:

R.Bager et al. (2013). Protein conformational change delayed by steric hindrance from an N-linked glycan. J Mol Biol, 425, 2867-2877. PubMed id: 23702291 DOI: 10.1016/j.jmb.2013.05.007

Date:

21-Feb-12 Release date: 27-Mar-13

Protein chains

F1QRB8  (F1QRB8_DANRE) -  Plasminogen activator inhibitor 1 from Danio rerio

Seq: 392 a.a.

Struc: 374 a.a.

DOI no: 10.1016/j.jmb.2013.05.007

J Mol Biol 425:2867-2877 (2013)

PubMed id: 23702291

Protein conformational change delayed by steric hindrance from an N-linked glycan.

R.Bager, J.S.Johansen, J.K.Jensen, A.Stensballe, A.Jendroszek, L.Buxbom, H.P.Sørensen, P.A.Andreasen.

ABSTRACT

Very few studies have attributed a direct, active, functional role to N-linked glycans. We describe here an N-linked glycan with a unique role for maintaining the active conformation of a protein of the serpin family. The distinguishing feature of serpins is the "stressed-to-relaxed" transition, in which the reactive center loop inserts as a β-strand into the central β-sheet A. This transition forms the basis for the conversion of serpins to the inactive latent state. We demonstrate that plasminogen activator inhibitor-1 (PAI-1) from zebrafish converts to the latent state about 5-fold slower than human PAI-1. In contrast to human PAI-1, fish PAI-1 carries a single N-linked glycan at Asn185 in the gate region through which the reactive center loop passes during latency transition. While the latency transition of human PAI-1 is unaffected by deglycosylation, deglycosylated zebrafish PAI-1 (zfPAI-1) goes latent about 50-fold faster than the glycosylated zfPAI-1 and about 25-fold faster than non-glycosylated human PAI-1. X-ray crystal structure analysis of glycosylated fish PAI-1 confirmed the presence of an N-linked glycan in the gate region and a lack of glycan-induced structural changes. Thus, latency transition of zfPAI-1 is delayed by steric hindrance from the glycan in the gate region. Our findings reveal a previously unknown mechanism for inhibition of protein conformational changes by steric hindrance from N-linked glycans.