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DOI no:
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J Mol Biol
177:531-557
(1984)
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PubMed id:
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Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function.
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H.Loebermann,
R.Tokuoka,
J.Deisenhofer,
R.Huber.
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ABSTRACT
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Two closely related crystal structures of alpha 1-proteinase inhibitor modified
at the reactive site peptide bond Met358--Ser359 have been analysed. The crystal
structure has been obtained from diffraction data at 3 A resolution, with phases
originally from isomorphous replacement. The electron density map was
substantially improved by cyclic averaging of the electron densities of the two
crystal forms and allowed the chain to be traced in terms of the known chemical
amino acid sequence. Energy restrained crystallographic refinement was initiated
and resulted in conventional R-values of 0.251 for the tetragonal crystal form
(6 to 3 A resolution) and 0.247 for the hexagonal crystal form (6 to 3.2 A
resolution). The polypeptide chain is almost completely arranged in well-defined
secondary structural elements: three beta-sheets and eight alpha-helices. The
helices are preferentially formed by the first 150 residues. They are in
proximity underneath sheet A. The chain ends Met358 and Ser359 of the nicked
species are arranged in strands on opposite ends of the molecule indicating a
major structural rearrangement upon modification of the intact inhibitor. It is
suggested that the Met358 strand is in a different conformation removed from
sheet A and approaches Ser359 in the intact inhibitor species. Glu342, which is
exchanged by a lysine in the Z-variant is in a strategic position for such a
rearrangement. The three carbohydrate chains of alpha 1-proteinase inhibitor
have partly defined electron density close to their attachment sites at
asparagine residues. The anti-thrombin and ovalbumin amino acid sequences can be
accommodated in the alpha 1 inhibitor molecular structure. The intron-exon
junctions of the ovalbumin and the alpha 1-proteinase inhibitor gene are all in
surface loops of the mature protein.
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Selected figure(s)
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Figure 4.
IG. 4. (a) and (b) Stereo diagram of the arrangement of sheets A to C. (Figs 3(b), 3(c), 4(b) and 5
were produced with a program by Lesk & Hardman (1982).)
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Figure 6.
FIG. 6. Stereo diagrams of the distribution of (a) apolar, (1)) acidic and (c) basic residues in
cc,-proteinase inhibitor.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1984,
177,
531-557)
copyright 1984.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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| |
PubMed id
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Reference
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PDB code:
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D.Ivanov,
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R.L.Moritz,
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S.Janciauskiene,
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T.H.Roberts,
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Serpin polymerization is prevented by a hydrogen bond network that is centered on his-334 and stabilized by glycerol.
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| |
J Biol Chem,
278,
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|
PDB code:
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|
|
|
|
|
|
|
D.T.Berg,
B.Gerlitz,
J.Shang,
T.Smith,
P.Santa,
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K.Mace,
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Proc Natl Acad Sci U S A,
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E.Marszal,
D.Danino,
and
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A novel mode of polymerization of alpha1-proteinase inhibitor.
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J Biol Chem,
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F.Tani,
N.Shirai,
Y.Nakanishi,
and
N.Kitabatake
(2003).
Analysis of molecular interactions in heat-induced aggregation of a non-inhibitory serpin ovalbumin using a molecular chaperone.
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| |
Biosci Biotechnol Biochem,
67,
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|
|
|
|
H.Yamamoto,
N.Takahashi,
M.Yamasaki,
Y.Arii,
and
M.Hirose
(2003).
Thermostabilization of ovalbumin by an alkaline treatment: examination for the possible implications of an altered serpin loop structure.
|
| |
Biosci Biotechnol Biochem,
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|
|
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|
|
|
J.A.Huntington
(2003).
Mechanisms of glycosaminoglycan activation of the serpins in hemostasis.
|
| |
J Thromb Haemost,
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M.Wilczynska,
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and
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EMBO J,
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Measurement of both native and inactivated forms of alpha1 proteinase inhibitor in human inflammatory extracellular fluids.
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J Clin Periodontol,
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A.A.Komissarov,
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Mechanisms of conversion of plasminogen activator inhibitor 1 from a suicide inhibitor to a substrate by monoclonal antibodies.
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J Biol Chem,
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E.J.Seo,
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Concerted regulation of inhibitory activity of alpha 1-antitrypsin by the native strain distributed throughout the molecule.
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J Biol Chem,
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Identification and characterization of a novel rat ov-serpin family member, trespin.
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J Biol Chem,
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Biophys J,
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L.Jankova,
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Crystal structure of the complex of plasminogen activator inhibitor 2 with a peptide mimicking the reactive center loop.
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| |
J Biol Chem,
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PDB code:
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M.K.Chow,
G.L.Devlin,
and
S.P.Bottomley
(2001).
Osmolytes as modulators of conformational changes in serpins.
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Biol Chem,
382,
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(2001).
Mechanism-based inactivation of caspases by the apoptotic suppressor p35.
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Biochemistry,
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S.Janciauskiene
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Conformational properties of serine proteinase inhibitors (serpins) confer multiple pathophysiological roles.
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Biochim Biophys Acta,
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S.Ye,
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M.R.Kanost,
and
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(2001).
The structure of a Michaelis serpin-protease complex.
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| |
Nat Struct Biol,
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PDB codes:
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C.Green,
E.Levashina,
C.McKimmie,
T.Dafforn,
J.M.Reichhart,
and
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(2000).
The necrotic gene in Drosophila corresponds to one of a cluster of three serpin transcripts mapping at 43A1.2.
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Genetics,
156,
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D.A.Lawrence,
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D.E.Day,
J.O.Kvassman,
D.Ginsburg,
and
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(2000).
Partitioning of serpin-proteinase reactions between stable inhibition and substrate cleavage is regulated by the rate of serpin reactive center loop insertion into beta-sheet A.
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J Biol Chem,
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G.C.Schussler
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Thyroid,
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Respir Med,
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M.W.Parker,
and
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| |
Protein Sci,
9,
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|
|
PDB code:
|
|
|
|
|
|
|
|
M.Fa,
F.Bergström,
P.Hägglöf,
M.Wilczynska,
L.B.Johansson,
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Structure,
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M.Renatus,
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S.J.Snipas,
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L.A.Bankston,
R.C.Liddington,
and
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(2000).
Crystal structure of the apoptotic suppressor CrmA in its cleaved form.
|
| |
Structure,
8,
789-797.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Mellet,
and
J.G.Bieth
(2000).
Evidence that translocation of the proteinase precedes its acylation in the serpin inhibition pathway.
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J Biol Chem,
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T.R.Dafforn,
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(2000).
Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease.
|
| |
Protein Sci,
9,
1274-1281.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.R.Hwang,
B.Steineckert,
and
V.Y.Hook
(2000).
Expression and mutagenesis of the novel serpin endopin 2 demonstrates a requirement for cysteine-374 for dithiothreitol-sensitive inhibition of elastase.
|
| |
Biochemistry,
39,
8944-8952.
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S.Yakovlev,
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D.Loukinov,
and
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(2000).
Role of the beta-strand insert in the central domain of the fibrinogen gamma-module.
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| |
Biochemistry,
39,
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A.M.Sharp,
P.E.Stein,
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M.B.Berkenpas,
D.Ginsburg,
D.A.Lawrence,
and
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(1999).
The active conformation of plasminogen activator inhibitor 1, a target for drugs to control fibrinolysis and cell adhesion.
|
| |
Structure,
7,
111-118.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.L.James,
J.C.Whisstock,
M.G.Gore,
and
S.P.Bottomley
(1999).
Probing the unfolding pathway of alpha1-antitrypsin.
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| |
J Biol Chem,
274,
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H.Im,
E.J.Seo,
and
M.H.Yu
(1999).
Metastability in the inhibitory mechanism of human alpha1-antitrypsin.
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| |
J Biol Chem,
274,
11072-11077.
|
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|
J.C.Whisstock,
J.A.Irving,
S.P.Bottomley,
R.N.Pike,
and
A.M.Lesk
(1999).
Serpins in the Caenorhabditis elegans genome.
|
| |
Proteins,
36,
31-41.
|
|
|
|
|
|
|
J.Li,
Z.Wang,
B.Canagarajah,
H.Jiang,
M.Kanost,
and
E.J.Goldsmith
(1999).
The structure of active serpin 1K from Manduca sexta.
|
| |
Structure,
7,
103-109.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.J.Harrop,
L.Jankova,
M.Coles,
D.Jardine,
J.S.Whittaker,
A.R.Gould,
A.Meister,
G.C.King,
B.C.Mabbutt,
and
P.M.Curmi
(1999).
The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: implications for serpin function.
|
| |
Structure,
7,
43-54.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.R.Dafforn,
R.Mahadeva,
P.R.Elliott,
P.Sivasothy,
and
D.A.Lomas
(1999).
A kinetic mechanism for the polymerization of alpha1-antitrypsin.
|
| |
J Biol Chem,
274,
9548-9555.
|
|
|
|
|
|
|
V.Picard,
P.E.Marque,
F.Paolucci,
M.Aiach,
and
B.F.Le Bonniec
(1999).
Topology of the stable serpin-protease complexes revealed by an autoantibody that fails to react with the monomeric conformers of antithrombin.
|
| |
J Biol Chem,
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PDB code:
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W.Bode,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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