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Contents |
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* Residue conservation analysis
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PDB id:
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Complex (proteinase/inhibitor)
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Title:
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Three-dimensional structure of the complex between pancreatic secretory inhibitor (kazal type) and trypsinogen at 1.8 angstroms resolution. Structure solution, crystallographic refinement and preliminary structural interpretation
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Structure:
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Trypsinogen. Chain: z. Engineered: yes. Pancreatic secretory trypsin inhibitor (kazal type). Chain: i. Engineered: yes
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Source:
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Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Sus scrofa. Pig. Organism_taxid: 9823
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Biol. unit:
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Dimer (from
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Resolution:
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Authors:
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M.Bolognesi,G.Gatti,E.Menegatti,M.Guarneri,M.Marquart,E.Papamokos, R.Huber
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Key ref:
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M.Bolognesi
et al.
(1982).
Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (Kazal type) and trypsinogen at 1.8 A resolution. Structure solution, crystallographic refinement and preliminary structural interpretation.
J Mol Biol,
162,
839-868.
PubMed id:
DOI:
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Date:
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27-Sep-82
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Release date:
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18-Jan-83
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PROCHECK
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Headers
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References
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Enzyme class:
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Chain Z:
E.C.3.4.21.4
- trypsin.
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Reaction:
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Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
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DOI no:
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J Mol Biol
162:839-868
(1982)
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PubMed id:
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Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (Kazal type) and trypsinogen at 1.8 A resolution. Structure solution, crystallographic refinement and preliminary structural interpretation.
|
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M.Bolognesi,
G.Gatti,
E.Menagatti,
M.Guarneri,
M.Marquart,
E.Papamokos,
R.Huber.
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ABSTRACT
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Selected figure(s)
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Figure 1.
FIG:. 1. (a) Trsnslation functon, plane = l/Z; (b) translation function, plane y = l/2; (c) translation
function, plane z = /2.
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Figure 7.
FIG. 7. Overlay of the 20-98 lop of trypsinogn. Filled lines depict the %dimensiona,l structure found
in trypsinogen. Open lines refer to the structure of activated trypsin.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1982,
162,
839-868)
copyright 1982.
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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
|
|
|
|
|
|
C.M.Ou,
S.R.Lin,
H.J.Lin,
C.W.Luo,
and
Y.H.Chen
(2010).
Exclusive expression of a membrane-bound Spink3-interacting serine protease-like protein TESPL in mouse testis.
|
| |
J Cell Biochem,
110,
620-629.
|
|
|
|
|
|
|
E.S.Park,
W.A.Fenton,
and
A.L.Horwich
(2007).
Disulfide formation as a probe of folding in GroEL-GroES reveals correct formation of long-range bonds and editing of incorrect short-range ones.
|
| |
Proc Natl Acad Sci U S A,
104,
2145-2150.
|
|
|
|
|
|
|
B.Xie,
E.Tassi,
M.R.Swift,
K.McDonnell,
E.T.Bowden,
S.Wang,
Y.Ueda,
Y.Tomita,
A.T.Riegel,
and
A.Wellstein
(2006).
Identification of the fibroblast growth factor (FGF)-interacting domain in a secreted FGF-binding protein by phage display.
|
| |
J Biol Chem,
281,
1137-1144.
|
|
|
|
|
|
|
F.Meier-Abt,
Y.Mokrab,
and
K.Mizuguchi
(2005).
Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode.
|
| |
J Membr Biol,
208,
213-227.
|
|
|
|
|
|
|
S.Yasuda,
N.Morokawa,
G.W.Wong,
A.Rossi,
M.S.Madhusudhan,
A.Sali,
Y.S.Askew,
R.Adachi,
G.A.Silverman,
S.A.Krilis,
and
R.L.Stevens
(2005).
Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22.
|
| |
Blood,
105,
3893-3901.
|
|
|
|
|
|
|
C.W.Luo,
H.J.Lin,
S.C.Gopinath,
and
Y.H.Chen
(2004).
Distinction of sperm-binding site and reactive site for trypsin inhibition on p12 secreted from the accessory sex glands of male mice.
|
| |
Biol Reprod,
70,
965-971.
|
|
|
|
|
|
|
C.A.Innis,
and
M.Hyvönen
(2003).
Crystal structures of the heparan sulfate-binding domain of follistatin. Insights into ligand binding.
|
| |
J Biol Chem,
278,
39969-39977.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.Liepinsh,
L.Banyai,
G.Pintacuda,
M.Trexler,
L.Patthy,
and
G.Otting
(2003).
NMR structure of the netrin-like domain (NTR) of human type I procollagen C-proteinase enhancer defines structural consensus of NTR domains and assesses potential proteinase inhibitory activity and ligand binding.
|
| |
J Biol Chem,
278,
25982-25989.
|
|
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PDB code:
|
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|
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|
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I.H.Barrette-Ng,
K.K.Ng,
M.M.Cherney,
G.Pearce,
C.A.Ryan,
and
M.N.James
(2003).
Structural basis of inhibition revealed by a 1:2 complex of the two-headed tomato inhibitor-II and subtilisin Carlsberg.
|
| |
J Biol Chem,
278,
24062-24071.
|
|
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PDB code:
|
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|
|
|
|
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I.H.Barrette-Ng,
K.K.Ng,
M.M.Cherney,
G.Pearce,
U.Ghani,
C.A.Ryan,
and
M.N.James
(2003).
Unbound form of tomato inhibitor-II reveals interdomain flexibility and conformational variability in the reactive site loops.
|
| |
J Biol Chem,
278,
31391-31400.
|
|
|
PDB code:
|
|
|
|
|
|
|
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H.Hemmi,
T.Yoshida,
T.Kumazaki,
N.Nemoto,
J.Hasegawa,
F.Nishioka,
Y.Kyogoku,
H.Yokosawa,
and
Y.Kobayashi
(2002).
Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy.
|
| |
Biochemistry,
41,
10657-10664.
|
|
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PDB code:
|
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|
|
|
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|
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L.Lu,
H.Lu,
and
J.Skolnick
(2002).
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
|
| |
Proteins,
49,
350-364.
|
|
|
|
|
|
|
N.S.Quinsey,
J.C.Whisstock,
B.Le Bonniec,
V.Louvain,
S.P.Bottomley,
and
R.N.Pike
(2002).
Molecular determinants of the mechanism underlying acceleration of the interaction between antithrombin and factor Xa by heparin pentasaccharide.
|
| |
J Biol Chem,
277,
15971-15978.
|
|
|
|
|
|
|
A.Pasternak,
A.White,
C.J.Jeffery,
N.Medina,
M.Cahoon,
D.Ringe,
and
L.Hedstrom
(2001).
The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity.
|
| |
Protein Sci,
10,
1331-1342.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
V.Z.Pletnev,
T.S.Zamolodchikova,
W.A.Pangborn,
and
W.L.Duax
(2000).
Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
|
| |
Proteins,
41,
8.
|
|
|
PDB code:
|
|
|
|
|
|
|
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Y.Li,
H.Li,
S.J.Smith-Gill,
and
R.A.Mariuzza
(2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
|
| |
Biochemistry,
39,
6296-6309.
|
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PDB codes:
|
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|
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A.Lombardi,
G.De Simone,
S.Galdiero,
N.Staiano,
F.Nastri,
and
V.Pavone
(1999).
From natural to synthetic multisite thrombin inhibitors.
|
| |
Biopolymers,
51,
19-39.
|
|
|
|
|
|
|
A.Pasternak,
D.Ringe,
and
L.Hedstrom
(1999).
Comparison of anionic and cationic trypsinogens: the anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure.
|
| |
Protein Sci,
8,
253-258.
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PDB codes:
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C.P.Sommerhoff,
W.Bode,
P.J.Pereira,
M.T.Stubbs,
J.Stürzebecher,
G.P.Piechottka,
G.Matschiner,
and
A.Bergner
(1999).
The structure of the human betaII-tryptase tetramer: fo(u)r better or worse.
|
| |
Proc Natl Acad Sci U S A,
96,
10984-10991.
|
|
|
|
|
|
|
D.C.Whitcomb
(1999).
Hereditary pancreatitis: new insights into acute and chronic pancreatitis.
|
| |
Gut,
45,
317-322.
|
|
|
|
|
|
|
D.J.Diller,
M.R.Redinbo,
E.Pohl,
and
W.G.Hol
(1999).
A database method for automated map interpretation in protein crystallography.
|
| |
Proteins,
36,
526-541.
|
|
|
|
|
|
|
H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
|
| |
Eur J Biochem,
260,
571-595.
|
|
|
|
|
|
|
H.Jing,
K.J.Macon,
D.Moore,
L.J.DeLucas,
J.E.Volanakis,
and
S.V.Narayana
(1999).
Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D.
|
| |
EMBO J,
18,
804-814.
|
|
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PDB code:
|
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|
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J.A.Cuff,
and
G.J.Barton
(1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
|
| |
Proteins,
34,
508-519.
|
|
|
|
|
|
|
R.Helland,
G.I.Berglund,
J.Otlewski,
W.Apostoluk,
O.A.Andersen,
N.P.Willassen,
and
A.O.Smalås
(1999).
High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
139-148.
|
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PDB codes:
|
|
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|
|
|
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A.Pasternak,
X.Liu,
T.Y.Lin,
and
L.Hedstrom
(1998).
Activating a zymogen without proteolytic processing: mutation of Lys15 and Asn194 activates trypsinogen.
|
| |
Biochemistry,
37,
16201-16210.
|
|
|
|
|
|
|
A.R.Khan,
and
M.N.James
(1998).
Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes.
|
| |
Protein Sci,
7,
815-836.
|
|
|
|
|
|
|
S.M.Bell,
C.Bennett,
A.F.Markham,
and
N.J.Lench
(1998).
Evidence for a common mutation in hereditary pancreatitis.
|
| |
Mol Pathol,
51,
115-117.
|
|
|
|
|
|
|
T.Asao,
K.Takahashi,
and
M.Tashiro
(1998).
Interaction of second and third domains of Japanese quail ovomucoid with ten mammalian trypsins.
|
| |
Biochim Biophys Acta,
1387,
415-421.
|
|
|
|
|
|
|
V.Ascoli,
F.Nardi,
C.Carnovale Scalzo,
S.Signoretti,
A.Pistilli,
and
F.Lo Coco
(1998).
Absence of HHV-8 DNA sequences in malignant mesothelioma.
|
| |
Mol Pathol,
51,
113-114.
|
|
|
|
|
|
|
A.Pandya,
X.J.Xia,
S.H.Blanton,
B.Landa,
T.Markello,
and
W.E.Nance
(1997).
Implications of molecular diagnostic testing in families with hereditary pancreatitis.
|
| |
Genet Test,
1,
207-211.
|
|
|
|
|
|
|
G.T.DeKoster,
and
A.D.Robertson
(1997).
Thermodynamics of unfolding for Kazal-type serine protease inhibitors: entropic stabilization of ovomucoid first domain by glycosylation.
|
| |
Biochemistry,
36,
2323-2331.
|
|
|
|
|
|
|
M.Renatus,
R.A.Engh,
M.T.Stubbs,
R.Huber,
S.Fischer,
U.Kohnert,
and
W.Bode
(1997).
Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA.
|
| |
EMBO J,
16,
4797-4805.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.D.Dickinson,
C.R.Kelly,
and
W.Ruf
(1996).
Identification of surface residues mediating tissue factor binding and catalytic function of the serine protease factor VIIa.
|
| |
Proc Natl Acad Sci U S A,
93,
14379-14384.
|
|
|
|
|
|
|
D.C.Whitcomb,
M.C.Gorry,
R.A.Preston,
W.Furey,
M.J.Sossenheimer,
C.D.Ulrich,
S.P.Martin,
L.K.Gates,
S.T.Amann,
P.P.Toskes,
R.Liddle,
K.McGrath,
G.Uomo,
J.C.Post,
and
G.D.Ehrlich
(1996).
Hereditary pancreatitis is caused by a mutation in the cationic trypsinogen gene.
|
| |
Nat Genet,
14,
141-145.
|
|
|
|
|
|
|
J.Whisstock,
A.M.Lesk,
and
R.Carrell
(1996).
Modeling of serpin-protease complexes: antithrombin-thrombin, alpha 1-antitrypsin (358Met-->Arg)-thrombin, alpha 1-antitrypsin (358Met-->Arg)-trypsin, and antitrypsin-elastase.
|
| |
Proteins,
26,
288-303.
|
|
|
|
|
|
|
N.C.Singha,
N.Surolia,
and
A.Surolia
(1996).
On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation.
|
| |
Biosci Rep,
16,
1.
|
|
|
|
|
|
|
A.van de Locht,
D.Lamba,
M.Bauer,
R.Huber,
T.Friedrich,
B.Kröger,
W.Höffken,
and
W.Bode
(1995).
Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin.
|
| |
EMBO J,
14,
5149-5157.
|
|
|
PDB codes:
|
|
|
|
|
|
|
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J.Janin
(1995).
Elusive affinities.
|
| |
Proteins,
21,
30-39.
|
|
|
|
|
|
|
P.Ascenzi,
G.Amiconi,
W.Bode,
M.Bolognesi,
M.Coletta,
and
E.Menegatti
(1995).
Proteinase inhibitors from the European medicinal leech Hirudo medicinalis: structural, functional and biomedical aspects.
|
| |
Mol Aspects Med,
16,
215-313.
|
|
|
|
|
|
|
R.Male,
J.B.Lorens,
A.O.Smalås,
and
K.R.Torrissen
(1995).
Molecular cloning and characterization of anionic and cationic variants of trypsin from Atlantic salmon.
|
| |
Eur J Biochem,
232,
677-685.
|
|
|
|
|
|
|
A.O.Smalås,
E.S.Heimstad,
A.Hordvik,
N.P.Willassen,
and
R.Male
(1994).
Cold adaption of enzymes: structural comparison between salmon and bovine trypsins.
|
| |
Proteins,
20,
149-166.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.N.Bhat,
G.A.Bentley,
G.Boulot,
M.I.Greene,
D.Tello,
W.Dall'Acqua,
H.Souchon,
F.P.Schwarz,
R.A.Mariuzza,
and
R.J.Poljak
(1994).
Bound water molecules and conformational stabilization help mediate an antigen-antibody association.
|
| |
Proc Natl Acad Sci U S A,
91,
1089-1093.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Gudmundsdóttir,
E.Gudmundsdóttir,
S.Oskarsson,
J.B.Bjarnason,
A.K.Eakin,
and
C.S.Craik
(1993).
Isolation and characterization of cDNAs from Atlantic cod encoding two different forms of trypsinogen.
|
| |
Eur J Biochem,
217,
1091-1097.
|
|
|
|
|
|
|
C.A.Orengo,
and
J.M.Thornton
(1993).
Alpha plus beta folds revisited: some favoured motifs.
|
| |
Structure,
1,
105-120.
|
|
|
|
|
|
|
W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
|
| |
Eur J Biochem,
204,
433-451.
|
|
|
|
|
|
|
Y.Takeuchi,
T.Nonaka,
K.T.Nakamura,
S.Kojima,
K.Miura,
and
Y.Mitsui
(1992).
Crystal structure of an engineered subtilisin inhibitor complexed with bovine trypsin.
|
| |
Proc Natl Acad Sci U S A,
89,
4407-4411.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Eberle,
C.Sander,
W.Klaus,
B.Schmidt,
K.von Figura,
and
C.Peters
(1991).
The essential tyrosine of the internalization signal in lysosomal acid phosphatase is part of a beta turn.
|
| |
Cell,
67,
1203-1209.
|
|
|
|
|
|
|
M.Bolognesi,
L.Pugliese,
G.Gatti,
F.Frigerio,
A.Coda,
L.Antolini,
H.P.Schnebli,
E.Menegatti,
G.Amiconi,
and
P.Ascenzi
(1990).
X-ray crystal structure of the bovine alpha-chymotrypsin/eglin c complex at 2.6 A resolution.
|
| |
J Mol Recognit,
3,
163-168.
|
|
|
|
|
|
|
G.M.Clore,
and
A.M.Gronenborn
(1989).
Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy.
|
| |
Crit Rev Biochem Mol Biol,
24,
479-564.
|
|
|
|
|
|
|
T.E.Creighton,
and
N.J.Darby
(1989).
Functional evolutionary divergence of proteolytic enzymes and their inhibitors.
|
| |
Trends Biochem Sci,
14,
319-324.
|
|
|
|
|
|
|
P.Ascenzi,
M.Coletta,
G.Amiconi,
M.Bolognesi,
M.Guarneri,
and
E.Menegatti
(1988).
Zymogen activation: effect of peptides sequentially related to the bovine beta-trypsin N-terminus on Kazal inhibitor and benzamidine binding to bovine trypsinogen.
|
| |
J Mol Recognit,
1,
130-137.
|
|
|
|
|
|
|
W.Bode,
E.Papamokos,
and
D.Musil
(1987).
The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry.
|
| |
Eur J Biochem,
166,
673-692.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Braun
(1987).
Distance geometry and related methods for protein structure determination from NMR data.
|
| |
Q Rev Biophys,
19,
115-157.
|
|
|
|
|
|
|
E.Menegatti,
M.Bolognesi,
S.Scalia,
F.Bortolotti,
M.Guarneri,
and
P.Ascenzi
(1986).
Gabexate mesylate inhibition of serine proteases: thermodynamic and computer-graphics analysis.
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| |
J Pharm Sci,
75,
1171-1174.
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P.Ascenzi,
G.Amiconi,
M.Bolognesi,
E.Menegatti,
and
M.Guarneri
(1986).
Binding of porcine pancreatic secretory trypsin inhibitor to bovine beta-trypsin: a kinetic study.
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| |
Biopolymers,
25,
2325-2333.
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W.Bode,
A.Z.Wei,
R.Huber,
E.Meyer,
J.Travis,
and
S.Neumann
(1986).
X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.
|
| |
EMBO J,
5,
2453-2458.
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PDB code:
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J.Miller,
A.D.McLachlan,
and
A.Klug
(1985).
Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes.
|
| |
EMBO J,
4,
1609-1614.
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W.Bode,
O.Epp,
R.Huber,
M.Laskowski,
and
W.Ardelt
(1985).
The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3).
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| |
Eur J Biochem,
147,
387-395.
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PDB code:
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W.Bode,
J.Walter,
R.Huber,
H.R.Wenzel,
and
H.Tschesche
(1984).
The refined 2.2-A (0.22-nm) X-ray crystal structure of the ternary complex formed by bovine trypsinogen, valine-valine and the Arg15 analogue of bovine pancreatic trypsin inhibitor.
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| |
Eur J Biochem,
144,
185-190.
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PDB code:
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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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