PDBsum entry 1qmb

Serine protease inhibitor

PDB id: 1qmb

Contents

Protein chains

326 a.a. *

42 a.a. *

Waters ×17

* Residue conservation analysis

PDB id:

1qmb

Name:

Serine protease inhibitor

Title:

Cleaved alpha-1-antitrypsin polymer

Structure:

Alpha-1-antitrypsin. Chain: a. Fragment: residues 49-69,71-302,304-376. Synonym: alpha-1-proteinase inhibitor, alpha-1-pi. Engineered: yes. Mutation: yes. Alpha-1-antitrypsin. Chain: b. Fragment: residues 377-418.

Source:

Homo sapiens. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.212 R-free: 0.258

Authors:

J.A.Huntington,N.S.Pannu,B.Hazes,R.J.Read,D.A.Lomas,R.W.Carrell

Key ref:

J.A.Huntington et al. (1999). A 2.6 A structure of a serpin polymer and implications for conformational disease. J Mol Biol, 293, 449-455. PubMed id: 10543942 DOI: 10.1006/jmbi.1999.3184

Date:

24-Sep-99 Release date: 06-Feb-00

Protein chain

P01009  (A1AT_HUMAN) -  Alpha-1-antitrypsin from Homo sapiens

Seq: 418 a.a.

Struc: 326 a.a.*

Protein chain

P01009  (A1AT_HUMAN) -  Alpha-1-antitrypsin from Homo sapiens

Seq: 418 a.a.

Struc: 42 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1006/jmbi.1999.3184

J Mol Biol 293:449-455 (1999)

PubMed id: 10543942

A 2.6 A structure of a serpin polymer and implications for conformational disease.

J.A.Huntington, N.S.Pannu, B.Hazes, R.J.Read, D.A.Lomas, R.W.Carrell.

ABSTRACT

The function of the serpins as proteinase inhibitors depends on their ability to insert the cleaved reactive centre loop as the fourth strand in the main A beta-sheet of the molecule upon proteolytic attack at the reactive centre, P1-P1'. This mechanism is vulnerable to mutations which result in inappropriate intra- or intermolecular loop insertion in the absence of cleavage. Intermolecular loop insertion is known as serpin polymerisation and results in a variety of diseases, most notably liver cirrhosis resulting from mutations of the prototypical serpin alpha1-antitrypsin. We present here the 2.6 A structure of a polymer of alpha1-antitrypsin cleaved six residues N-terminal to the reactive centre, P7-P6 (Phe352-Leu353). After self insertion of P14 to P7, intermolecular linkage is affected by insertion of the P6-P3 residues of one molecule into the partially occupied beta-sheet A of another. This results in an infinite, linear polymer which propagates in the crystal along a 2-fold screw axis. These findings provide a framework for understanding the uncleaved alpha1-antitrypsin polymer and fibrillar and amyloid deposition of proteins seen in other conformational diseases, with the ordered array of polymers in the crystal resulting from slow accretion of the cleaved serpin over the period of a year.

Selected figure(s)

Figure 1.
Figure 1. (a) Monomer of the P7-P6 cleaved Pittsburgh a[1]-antitrypsin in the classical view with b-sheet A in blue and the portion of the reactive centre loop which becomes strand 4A after cleavage in red. The normal scissile bond (P1-P1') is indicated by the arrow. Cleavage at this site results in a full occupancy of b-sheet A with the inclusion of residues P15 through P3 as s4A. The P7 and P6 residues are indicated and are separated by 70 Å. The effect of cleavage at P7-P6 is a partial occupancy of the strand 4A allowing for ready insertion of the residues C-terminal to the cleavage site, P6*-P3*, from another monomer. (b) Such intermolecular loop insertion is demonstrated in the structure of a tetramer extracted from the infinite polymer, with the P6-P3 segment of one monomer clearly visible within the b-sheet A of the other. Insertion is in register with P1-P1' cleaved a[1]-antitrypsin. The monomers which compose the polymer are related in the crystal by a 2[1]-fold screw axis parallel to the Image cell edge. (c) The view down the 3[1]-fold screw axis of the crystal lattice reveals its tube-like nature. The unusually high solvent content of 73 % is explained by the 108 Å diameter hole that extends for the length of the crystal. (d) The current model of the uncleaved a[1]-antitrypsin trimer (magenta) [Elliott et al 1996 and Mahadeva et al 1999] and the structure of the cleaved a[1]-antitrypsin trimer (cyan) in space-filling representation after superposition of the first monomer. Polymerisation for the uncleaved model is affected by in register insertion of the P8 to P3 of the reactive centre loop into the b-sheet A of the following monomer. The model is thus constrained and cannot adopt the conformation of the cleaved polymer with which it is morphologically similar by electron microscopy. The Figures were generated using Molscript [Kraulis 1991] and Raster3D [Bacon and Anderson 1988 and Merritt and Murphy 1994].

Figure 2.
Figure 2. (a) A stereo view of the cleaved a[1]-antitrypsin dimer with a s[A]-weighted omit map, contoured at four times the r.m.s. of the map, for the region extending from P15 to P5', shows the unequivocal nature of the dimer contact. Continuous density is observed for the entire length of strand 4A of the black monomer into strand 1C of the next monomer in green. Weak density is observed at the site of cleavage. (b) A close-up of the omit map at the site of cleavage. P15 to P7 is in black with P6* to P5'* of the dimer partner in green. The omit map was computed after refinement using the model of cleaved a[1]-antitrypsin with the reactive centre loop (P15-P5') removed.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 449-455) copyright 1999.