|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Complex (serine protease/inhibitor)
|
|
|
Title:
|
|
Structure of thrombin complexed with bovine pancreatic trypsin inhibitor
|
|
Structure:
|
|
Thrombin. Chain: l, j. Engineered: yes. Mutation: yes. Thrombin. Chain: h, k. Engineered: yes. Mutation: yes. Bovine pancreatic trypsin inhibitor.
|
|
Source:
|
|
Bos taurus. Cattle. Organism_taxid: 9913. Organ: lung. Expressed in: mesocricetus auratus. Expression_system_taxid: 10036. Expression_system_cell_line: bhk-21. Organ: lung
|
|
Biol. unit:
|
|
Trimer (from
)
|
|
Resolution:
|
|
|
2.30Å
|
R-factor:
|
0.196
|
R-free:
|
0.271
|
|
|
Authors:
|
|
A.Van De Locht,W.Bode,M.T.Stubbs
|
Key ref:
|
|
A.van de Locht
et al.
(1997).
The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.
Embo J,
16,
2977-2984.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
03-Dec-96
|
Release date:
|
24-Dec-97
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P00734
(THRB_HUMAN) -
Prothrombin from Homo sapiens
|
|
|
|
Seq:
Struc:
|
|
|
|
622 a.a.
31 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chains L, H, J, K:
E.C.3.4.21.5
- thrombin.
|
|
|
|
|
|
|
Reaction:
|
|
Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Embo J
16:2977-2984
(1997)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
The thrombin E192Q-BPTI complex reveals gross structural rearrangements: implications for the interaction with antithrombin and thrombomodulin.
|
|
A.van de Locht,
W.Bode,
R.Huber,
B.F.Le Bonniec,
S.R.Stone,
C.T.Esmon,
M.T.Stubbs.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Previous crystal structures of thrombin indicate that the 60-insertion loop is a
rigid moiety that partially occludes the active site, suggesting that this
structural feature plays a decisive role in restricting thrombin's specificity.
This restricted specificity is typified by the experimental observation that
thrombin is not inhibited by micromolar concentrations of basic pancreatic
trypsin inhibitor (BPTI). Surprisingly, a single atom mutation in thrombin
(E192Q) results in a 10(-8) M affinity for BPTI. The crystal structure of human
thrombin mutant E192Q has been solved in complex with BPTI at 2.3 A resolution.
Binding of the Kunitz inhibitor is accompanied by gross structural
rearrangements in thrombin. In particular, thrombin's 60-loop is found in a
significantly different conformation. Concomitant reorganization of other
surface loops that surround the active site, i.e. the 37-loop, the 148-loop and
the 99-loop, is observed. Thrombin can therefore undergo major structural
reorganization upon strong ligand binding. Implications for the interaction of
thrombin with antithrombin and thrombomodulin are discussed.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
Figure 1 Stereo view of the complex formed between human
thrombin E192Q (cyan) and BPTI (red). View is from the north
side with thrombin's 60-loop facing the viewer, i.e. rotated by
90° along x compared with thrombin's standard orientation shown
in Figure 3A. Disulfide bridges are displayed as yellow
connections. Figure prepared using MOLSCRIPT (Kraulis, 1991).
|
|
Figure 3.
Figure 3 Changes upon BPTI binding. (A) Stereo view of thrombin
in its standard orientation, i.e. with the active site cleft
facing the viewer and the 60-loop to the north. The unaltered
core of thrombin is shown with its molecular surface. Colour
coding indicates surface curvature with concave regions in blue
and convex regions in white. Loops whose position is affected
upon BPTI binding are depicted as rods. Colour coding is green
for PPACK -thrombin and orange for BPTI -thrombin. Residues of
the catalytic triad and Gln192 are also shown. Figure produced
with Grasp (Nicholls et al., 1993). (B) Close up of the
alterations in the 60- and 39-loops upon BPTI binding. Colour
coding is as in (A). Thin blue lines indicate the unaltered
thrombin core.
|
|
|
|
|
|
| |
The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Embo J
(1997,
16,
2977-2984)
copyright 1997.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.Eigenbrot,
R.Ganesan,
and
D.Kirchhofer
(2010).
Hepatocyte growth factor activator (HGFA): molecular structure and interactions with HGFA inhibitor-1 (HAI-1).
|
| |
FEBS J,
277,
2215-2222.
|
|
|
|
|
|
|
H.L.de Amorim,
P.A.Netz,
and
J.A.Guimarães
(2010).
Thrombin allosteric modulation revisited: a molecular dynamics study.
|
| |
J Mol Model,
16,
725-735.
|
|
|
|
|
|
|
E.Di Cera
(2008).
Thrombin.
|
| |
Mol Aspects Med,
29,
203-254.
|
|
|
|
|
|
|
M.G.Lerner,
K.L.Meagher,
and
H.A.Carlson
(2008).
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design.
|
| |
J Comput Aided Mol Des,
22,
727-736.
|
|
|
|
|
|
|
S.Macedo-Ribeiro,
C.Almeida,
B.M.Calisto,
T.Friedrich,
R.Mentele,
J.Stürzebecher,
P.Fuentes-Prior,
and
P.J.Pereira
(2008).
Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick.
|
| |
PLoS ONE,
3,
e1624.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Bah,
Z.Chen,
L.A.Bush-Pelc,
F.S.Mathews,
and
E.Di Cera
(2007).
Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
|
| |
Proc Natl Acad Sci U S A,
104,
11603-11608.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Y.Wu,
C.Eigenbrot,
W.C.Liang,
S.Stawicki,
S.Shia,
B.Fan,
R.Ganesan,
M.T.Lipari,
and
D.Kirchhofer
(2007).
Structural insight into distinct mechanisms of protease inhibition by antibodies.
|
| |
Proc Natl Acad Sci U S A,
104,
19784-19789.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.C.Castro,
R.Q.Monteiro,
M.Assafim,
N.I.Loureiro,
C.Craik,
and
R.B.Zingali
(2006).
Ecotin modulates thrombin activity through exosite-2 interactions.
|
| |
Int J Biochem Cell Biol,
38,
1893-1900.
|
|
|
|
|
|
|
D.Navaneetham,
L.Jin,
P.Pandey,
J.E.Strickler,
R.E.Babine,
S.S.Abdel-Meguid,
and
P.N.Walsh
(2005).
Structural and mutational analyses of the molecular interactions between the catalytic domain of factor XIa and the Kunitz protease inhibitor domain of protease nexin 2.
|
| |
J Biol Chem,
280,
36165-36175.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
|
| |
Proteins,
59,
580-591.
|
|
|
|
|
|
|
W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
|
| |
J Thromb Haemost,
3,
2379-2388.
|
|
|
|
|
|
|
A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
|
| |
Proteins,
56,
130-142.
|
|
|
|
|
|
|
A.O.Pineda,
C.J.Carrell,
L.A.Bush,
S.Prasad,
S.Caccia,
Z.W.Chen,
F.S.Mathews,
and
E.Di Cera
(2004).
Molecular dissection of Na+ binding to thrombin.
|
| |
J Biol Chem,
279,
31842-31853.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.De Cristofaro,
S.Akhavan,
C.Altomare,
A.Carotti,
F.Peyvandi,
and
P.M.Mannucci
(2004).
A natural prothrombin mutant reveals an unexpected influence of A-chain structure on the activity of human alpha-thrombin.
|
| |
J Biol Chem,
279,
13035-13043.
|
|
|
|
|
|
|
A.Dementiev,
M.Simonovic,
K.Volz,
and
P.G.Gettins
(2003).
Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases.
|
| |
J Biol Chem,
278,
37881-37887.
|
|
|
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.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Heifetz,
E.Katchalski-Katzir,
and
M.Eisenstein
(2002).
Electrostatics in protein-protein docking.
|
| |
Protein Sci,
11,
571-587.
|
|
|
|
|
|
|
C.Gaboriaud,
V.Rossi,
I.Bally,
G.J.Arlaud,
and
J.C.Fontecilla-Camps
(2000).
Crystal structure of the catalytic domain of human complement c1s: a serine protease with a handle.
|
| |
EMBO J,
19,
1755-1765.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.Favre,
G.W.Moss,
D.P.Goldenberg,
J.Otlewski,
and
E.Moczydlowski
(2000).
Structure-activity relationships for the interaction of bovine pancreatic trypsin inhibitor with an intracellular site on a large conductance Ca(2+)-activated K(+) channel.
|
| |
Biochemistry,
39,
2001-2012.
|
|
|
|
|
|
|
J.R.Hesselberth,
D.Miller,
J.Robertus,
and
A.D.Ellington
(2000).
In vitro selection of RNA molecules that inhibit the activity of ricin A-chain.
|
| |
J Biol Chem,
275,
4937-4942.
|
|
|
|
|
|
|
P.E.Marque,
R.Spuntarelli,
L.Juliano,
M.Aiach,
and
B.F.Le Bonniec
(2000).
The role of Glu(192) in the allosteric control of the S(2)' and S(3)' subsites of thrombin.
|
| |
J Biol Chem,
275,
809-816.
|
|
|
|
|
|
|
R.Krishnan,
I.Mochalkin,
R.Arni,
and
A.Tulinsky
(2000).
Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
294-303.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
|
| |
Eur J Biochem,
260,
571-595.
|
|
|
|
|
|
|
I.Mochalkin,
and
A.Tulinsky
(1999).
Structures of thrombin retro-inhibited with SEL2711 and SEL2770 as they relate to factor Xa binding.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
785-793.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.A.Kolkman,
O.D.Christophe,
P.J.Lenting,
and
K.Mertens
(1999).
Surface loop 199-204 in blood coagulation factor IX is a cofactor-dependent site involved in macromolecular substrate interaction.
|
| |
J Biol Chem,
274,
29087-29093.
|
|
|
|
|
|
|
K.E.Knobe,
A.Berntsdotter,
L.Shen,
J.Morser,
B.Dahlbäck,
and
B.O.Villoutreix
(1999).
Probing the activation of protein C by the thrombin-thrombomodulin complex using structural analysis, site-directed mutagenesis, and computer modeling.
|
| |
Proteins,
35,
218-234.
|
|
|
|
|
|
|
R.De Cristofaro,
and
R.Landolfi
(1999).
Allosteric modulation of BPTI interaction with human alpha- and zeta-thrombin.
|
| |
Eur J Biochem,
260,
97.
|
|
|
|
|
|
|
A.R.Rezaie
(1998).
Elucidation of the structural basis for the slow reactivity of thrombin with plasminogen activator inhibitor-1.
|
| |
Biochemistry,
37,
13138-13142.
|
|
|
|
|
|
|
J.H.Han,
and
D.M.Tollefsen
(1998).
Ligand binding to thrombin exosite II induces dissociation of the thrombin-heparin cofactor II(L444R) complex.
|
| |
Biochemistry,
37,
3203-3209.
|
|
|
|
|
|
|
N.S.Colwell,
M.A.Blinder,
M.Tsiang,
C.S.Gibbs,
P.E.Bock,
and
D.M.Tollefsen
(1998).
Allosteric effects of a monoclonal antibody against thrombin exosite II.
|
| |
Biochemistry,
37,
15057-15065.
|
|
|
|
|
|
|
R.Morenweiser,
E.A.Auerswald,
A.van de Locht,
H.Fritz,
J.Stürzebecher,
and
M.T.Stubbs
(1997).
Structure-based design of a potent chimeric thrombin inhibitor.
|
| |
J Biol Chem,
272,
19938-19942.
|
|
|
|
|
|
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.
|
 |
|
Links
