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PDBsum entry 1qmb
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Serine protease inhibitor
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PDB id
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1qmb
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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A 2.6 a structure of a serpin polymer and implications for conformational disease.
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Authors
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J.A.Huntington,
N.S.Pannu,
B.Hazes,
R.J.Read,
D.A.Lomas,
R.W.Carrell.
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Ref.
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J Mol Biol, 1999,
293,
449-455.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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].
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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.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
293,
449-455)
copyright 1999.
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