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Hydrolase(serine proteinase)
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PDB id
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2pf1
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.5
- Thrombin.
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Reaction:
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Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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1 term
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Biological process
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blood coagulation
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2 terms
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Biochemical function
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calcium ion binding
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2 terms
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DOI no:
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J Mol Biol
220:481-494
(1991)
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PubMed id:
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Structure of bovine prothrombin fragment 1 refined at 2.25 A resolution.
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T.P.Seshadri,
A.Tulinsky,
E.Skrzypczak-Jankun,
C.H.Park.
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ABSTRACT
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The structure of bovine prothrombin fragment 1 has been refined at 2.25 A
resolution using high resolution measurements made with the synchrotron beam at
CHESS. The synchrotron data were collected photographically by oscillation
methods (R-merge = 0.08). These were combined with lower order diffractometer
data for refinement purposes. The structure was refined using restrained
least-squares methods with the program PROLSQ to a crystallographic R-value of
0.175. The structure includes 105 water molecules with occupancies of greater
than 0.6. The first 35 residues (Ala1-Leu35) of the N-terminal gamma-carboxy
glutamic acid-domain (Ala1-Cys48) of fragment 1 are disordered as are two
carbohydrate chains of Mr approximately 5000; the latter two combine to render
40% of the structure disordered. The folding of the kringle of fragment 1 is
related to the close intramolecular contact between the inner loop disulfide
groups. Half of the conserved sequence of the kringle forms an inner core
surrounding these disulfide groups. The remainder of the sequence conservation
is associated with the many turns of the main chain. The Pro95 residue of the
kringle has a cis conformation and Tyr74 is ordered in fragment 1, although
nuclear magnetic resonance studies indicate that the comparable residue of
plasminogen kringle 4 has two positions. Surface accessibility calculations
indicate that none of the disulfide groups of fragment 1 is accessible to
solvent.
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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.H.Geiger,
and
S.E.Cnudde
(2004).
What the structure of angiostatin may tell us about its mechanism of action.
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J Thromb Haemost, 2,
23-34.
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M.Gehrmann,
K.Briknarová,
L.Bányai,
L.Patthy,
and
M.Llinás
(2002).
The col-1 module of human matrix metalloproteinase-2 (MMP-2): structural/functional relatedness between gelatin-binding fibronectin type II modules and lysine-binding kringle domains.
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Biol Chem, 383,
137-148.
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PDB code:
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H.Mizuno,
Z.Fujimoto,
M.Koizumi,
H.Kano,
H.Atoda,
and
T.Morita
(1997).
Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains.
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Nat Struct Biol, 4,
438-441.
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PDB code:
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A.van de Locht,
M.T.Stubbs,
M.Bauer,
and
W.Bode
(1996).
Crystallographic evidence that the F2 kringle catalytic domain linker of prothrombin does not cover the fibrinogen recognition exosite.
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J Biol Chem, 271,
3413-3416.
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J.Guevara,
N.V.Valentinova,
O.Garcia,
A.M.Gotto,
C.Y.Yang,
S.Legal,
J.Gaubatz,
and
J.T.Sparrow
(1996).
Interaction of apolipoprotein[a] with apolipoproteinB-100 Cys3734 region in lipoprotein[a] is confirmed immunochemically.
|
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J Protein Chem, 15,
17-25.
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M.Hof,
G.R.Fleming,
and
V.Fidler
(1996).
Time-resolved fluorescence study of a calcium-induced conformational change in prothrombin fragment 1.
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Proteins, 24,
485-494.
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W.K.Stevens,
H.F.Côté,
R.T.MacGillivray,
and
M.E.Nesheim
(1996).
Calcium ion modulation of meizothrombin autolysis at Arg55-Asp56 and catalytic activity.
|
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J Biol Chem, 271,
8062-8067.
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A.M.Scanu,
and
C.Edelstein
(1995).
Kringle-dependent structural and functional polymorphism of apolipoprotein (a).
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Biochim Biophys Acta, 1256,
1.
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H.Brandstetter,
M.Bauer,
R.Huber,
P.Lollar,
and
W.Bode
(1995).
X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.
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Proc Natl Acad Sci U S A, 92,
9796-9800.
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PDB code:
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M.T.Stubbs,
and
W.Bode
(1995).
The clot thickens: clues provided by thrombin structure.
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| |
Trends Biochem Sci, 20,
23-28.
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K.Padmanabhan,
T.P.Wu,
K.G.Ravichandran,
and
A.Tulinsky
(1994).
Kringle-kringle interactions in multimer kringle structures.
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Protein Sci, 3,
898-910.
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PDB codes:
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L.E.Donate,
E.Gherardi,
N.Srinivasan,
R.Sowdhamini,
S.Aparicio,
and
T.L.Blundell
(1994).
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).
|
| |
Protein Sci, 3,
2378-2394.
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M.T.Stubbs,
and
W.Bode
(1994).
Coagulation factors and their inhibitors.
|
| |
Curr Opin Struct Biol, 4,
823-832.
|
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J.Guevara,
J.Spurlino,
A.Y.Jan,
C.Y.Yang,
A.Tulinsky,
B.V.Prasad,
J.W.Gaubatz,
and
J.D.Morrisett
(1993).
Proposed mechanisms for binding of apo[a] kringle type 9 to apo B-100 in human lipoprotein[a].
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Biophys J, 64,
686-700.
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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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Links
