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PDBsum entry 1tie
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Proteinase inhibitor (trypsin)
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PDB id
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1tie
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Contents |
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* Residue conservation analysis
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J Mol Biol
217:153-176
(1991)
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PubMed id:
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Crystal structure of a Kunitz-type trypsin inhibitor from Erythrina caffra seeds.
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S.Onesti,
P.Brick,
D.M.Blow.
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ABSTRACT
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The trypsin inhibitor DE-3 from Erythrina caffra (ETI) belongs to the
Kunitz-type soybean trypsin inhibitor (STI) family and consists of 172 amino
acid residues with two disulphide bridges. The amino acid sequence of ETI shows
high homology to other trypsin inhibitors from the same family but ETI has the
unique ability to bind and inhibit tissue plasminogen activator. The crystal
structure of ETI has been determined using the method of isomorphous replacement
and refined using a combination of simulated annealing and conventional
restrained least-squares crystallographic refinement. The refined model includes
60 water molecules and 166 amino acid residues, with a root-mean-square
deviation in bond lengths from ideal values of 0.016 A. The crystallographic
R-factor is 20.8% for 7770 independent reflections between 10.0 and 2.5 A. The
three-dimensional structure of ETI consists of 12 antiparallel beta-strands
joined by long loops. Six of the strands form a short antiparallel beta-barrel
that is closed at one end by a "lid" consisting of the other six strands coupled
in pairs. The molecule shows approximate 3-fold symmetry about the axis of the
barrel, with the repeating unit consisting of four sequential beta-strands and
the connecting loops. Although there is no sequence homology, this same fold is
present in the structure of interleukin-1 alpha and interleukin-1 beta. When the
structure of ETI and interleukin-1 beta are superposed, the close agreement
between the alpha-carbon positions for the beta-strands is striking. The
scissile bond (Arg63-Ser64) is located on an external loop that protrudes from
the surface of the molecule and whose architecture is not constrained by
secondary structure elements, disulphide bridges or strong electrostatic
interactions. The hydrogen bonds made by the side-chain amide group of Asn12
play a key role in maintaining the three-dimensional structure of the loop. This
residue is in a position corresponding to that of a conserved asparagine in the
Kazal inhibitor family. Although the overall structure of ETI is similar to the
partial structure of STI, the scissile bond loop is displaced by about 4 A. This
displacement probably arises from the fact that the structure of STI has been
determined in a complex with trypsin but could possibly be a consequence of the
close molecular contact between Arg63 and an adjacent molecule in the crystal
lattice.
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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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J.M.Mondego,
M.P.Duarte,
E.Kiyota,
L.Martínez,
S.R.de Camargo,
F.P.De Caroli,
B.S.Alves,
S.M.Guerreiro,
M.L.Oliva,
O.Guerreiro-Filho,
and
M.Menossi
(2011).
Molecular characterization of a miraculin-like gene differentially expressed during coffee development and coffee leaf miner infestation.
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Planta,
233,
123-137.
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M.Renko,
J.Sabotic,
M.Mihelic,
J.Brzin,
J.Kos,
and
D.Turk
(2010).
Versatile loops in mycocypins inhibit three protease families.
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J Biol Chem,
285,
308-316.
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PDB codes:
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S.Khamrui,
S.Majumder,
J.Dasgupta,
J.K.Dattagupta,
and
U.Sen
(2010).
Identification of a novel set of scaffolding residues that are instrumental for the inhibitory property of Kunitz (STI) inhibitors.
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Protein Sci,
19,
593-602.
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PDB codes:
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R.Bao,
C.Z.Zhou,
C.Jiang,
S.X.Lin,
C.W.Chi,
and
Y.Chen
(2009).
The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation.
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J Biol Chem,
284,
26676-26684.
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PDB code:
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S.Roy,
and
S.K.Dutta
(2009).
Genomic and cDNA cloning, expression, purification, and characterization of chymotrypsin-trypsin inhibitor from winged bean seeds.
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Biosci Biotechnol Biochem,
73,
2671-2676.
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C.Jiang,
R.Bao,
and
Y.Chen
(2008).
Expression, purification, crystallization and preliminary X-ray diffraction analysis of Sagittaria sagittifolia arrowhead protease inhibitor API-A in complex with bovine trypsin.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
1060-1062.
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Y.H.Lin,
W.Y.Peng,
Y.C.Huang,
H.H.Guan,
Y.C.Hsieh,
M.Y.Liu,
T.Chang,
and
C.J.Chen
(2006).
Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
743-745.
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B.C.Bønsager,
P.K.Nielsen,
M.Abou Hachem,
K.Fukuda,
M.Praetorius-Ibba,
and
B.Svensson
(2005).
Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor.
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J Biol Chem,
280,
14855-14864.
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S.Iwanaga,
N.Yamasaki,
M.Kimura,
and
Y.Kouzuma
(2005).
Contribution of conserved Asn residues to the inhibitory activities of Kunitz-type protease inhibitors from plants.
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Biosci Biotechnol Biochem,
69,
220-223.
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O.L.Franco,
D.J.Rigden,
F.R.Melo,
and
M.F.Grossi-De-Sá
(2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
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Eur J Biochem,
269,
397-412.
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O.L.Franco,
M.F.Grossi de Sá,
M.P.Sales,
L.V.Mello,
A.S.Oliveira,
and
D.J.Rigden
(2002).
Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora.
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Proteins,
49,
335-341.
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I.F.Batista,
M.C.Nonato,
M.R.Bonfadini,
L.M.Beltramini,
M.L.Oliva,
M.U.Sampaio,
C.A.Sampaio,
and
R.C.Garratt
(2001).
Preliminary crystallographic studies of EcTI, a serine proteinase inhibitor from Enterolobium contortisiliquum seeds.
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Acta Crystallogr D Biol Crystallogr,
57,
602-604.
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S.R.Brych,
S.I.Blaber,
T.M.Logan,
and
M.Blaber
(2001).
Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.
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Protein Sci,
10,
2587-2599.
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PDB codes:
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K.W.Rodenburg,
F.Vallée,
N.Juge,
N.Aghajari,
X.Guo,
R.Haser,
and
B.Svensson
(2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
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Eur J Biochem,
267,
1019-1029.
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T.A.Valueva,
T.A.Revina,
V.V.Mosolov,
and
R.Mentele
(2000).
Primary structure of potato kunitz-type serine proteinase inhibitor.
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Biol Chem,
381,
1215-1221.
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I.Polikarpov,
A.M.Golubev,
L.A.Perles,
S.C.Pando,
J.C.Novello,
and
S.Marangoni
(1999).
Purification, crystallization and preliminary crystallographic study of a Kunitz-type trypsin inhibitor from Delonix regia seeds.
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Acta Crystallogr D Biol Crystallogr,
55,
1611-1613.
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J.K.Dattagupta,
A.Podder,
C.Chakrabarti,
U.Sen,
D.Mukhopadhyay,
S.K.Dutta,
and
M.Singh
(1999).
Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site.
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Proteins,
35,
321-331.
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PDB code:
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S.Ravichandran,
U.Sen,
C.Chakrabarti,
and
J.K.Dattagupta
(1999).
Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 A resolution.
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Acta Crystallogr D Biol Crystallogr,
55,
1814-1821.
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PDB code:
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F.Vallée,
A.Kadziola,
Y.Bourne,
M.Juy,
K.W.Rodenburg,
B.Svensson,
and
R.Haser
(1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
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Structure,
6,
649-659.
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PDB code:
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H.K.Song,
and
S.W.Suh
(1998).
Preliminary X-ray crystallographic analysis of Bowman-Birk trypsin inhibitor from barley seeds.
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Acta Crystallogr D Biol Crystallogr,
54,
441-443.
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T.D.Osslund,
R.Syed,
E.Singer,
E.W.Hsu,
R.Nybo,
B.L.Chen,
T.Harvey,
T.Arakawa,
L.O.Narhi,
A.Chirino,
and
C.F.Morris
(1998).
Correlation between the 1.6 A crystal structure and mutational analysis of keratinocyte growth factor.
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Protein Sci,
7,
1681-1690.
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M.Kimura,
N.Harada,
S.Iwanaga,
and
N.Yamasaki
(1997).
Analysis of the complex formed by Erythrina variegata chymotrypsin inhibitor with chymotrypsin and properties of the peptides prepared from the inhibitor by a limited proteolysis.
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Eur J Biochem,
249,
870-877.
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S.Di Marco,
and
J.P.Priestle
(1997).
Structure of the complex of leech-derived tryptase inhibitor (LDTI) with trypsin and modeling of the LDTI-tryptase system.
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Structure,
5,
1465-1474.
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PDB code:
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K.Lehle,
U.Kohnert,
A.Stern,
F.Popp,
and
R.Jaenicke
(1996).
Effect of disulfide bonds on the structure, function, and stability of the trypsin/tPA inhibitor from Erythrina caffra: site-directed mutagenesis, expression, and physiochemical characterization.
|
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Nat Biotechnol,
14,
476-480.
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S.Odani,
Y.Yokokawa,
H.Takeda,
S.Abe,
and
S.Odani
(1996).
The primary structure and characterization of carbohydrate chains of the extracellular glycoprotein proteinase inhibitor from latex of Carica papaya.
|
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Eur J Biochem,
241,
77-82.
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H.A.Schreuder,
J.M.Rondeau,
C.Tardif,
A.Soffientini,
E.Sarubbi,
A.Akeson,
T.L.Bowlin,
S.Yanofsky,
and
R.W.Barrett
(1995).
Refined crystal structure of the interleukin-1 receptor antagonist. Presence of a disulfide link and a cis-proline.
|
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Eur J Biochem,
227,
838-847.
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PDB code:
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K.Matsuoka,
D.C.Bassham,
N.V.Raikhel,
and
K.Nakamura
(1995).
Different sensitivity to wortmannin of two vacuolar sorting signals indicates the presence of distinct sorting machineries in tobacco cells.
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J Cell Biol,
130,
1307-1318.
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M.B.Swindells
(1995).
A procedure for the automatic determination of hydrophobic cores in protein structures.
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Protein Sci,
4,
93.
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J.M.Parker,
and
R.S.Hodges
(1994).
HomologyPlot: searching for homology to a family of proteins using a database of unique conserved patterns.
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J Comput Aided Mol Des,
8,
193-210.
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K.Huang,
N.C.Strynadka,
V.D.Bernard,
R.J.Peanasky,
and
M.N.James
(1994).
The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
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Structure,
2,
679-689.
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PDB code:
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A.E.Eriksson,
L.S.Cousens,
and
B.W.Matthews
(1993).
Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.
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Protein Sci,
2,
1274-1284.
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PDB codes:
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T.E.Creighton,
and
J.Kemmink
(1993).
NOGGIN is unlikely to be homologous to the Kunitz protease-inhibitor family.
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Trends Biochem Sci,
18,
424-426.
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S.Onesti,
D.J.Matthews,
P.Aducci,
G.Amiconi,
M.Bolognesi,
E.Menegatti,
and
P.Ascenzi
(1992).
Binding of the Kunitz-type trypsin inhibitor DE-3 from Erythrina caffra seeds to serine proteinases: a comparative study.
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J Mol Recognit,
5,
105-114.
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W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
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Eur J Biochem,
204,
433-451.
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F.L.Sebastiani,
L.B.Farrell,
M.Vasquez,
and
R.N.Beachy
(1991).
Conserved amino acid sequences among plant proteins sorted to protein bodies and plant vacuoles. Can they play a role in protein sorting?
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Eur J Biochem,
199,
441-450.
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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
codes are
shown on the right.
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Links
