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PDBsum entry 1ycp
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Hydrolase/hydrolase substrate
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PDB id
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1ycp
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Contents |
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29 a.a.
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247 a.a.
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146 a.a.
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101 a.a.
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* Residue conservation analysis
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PDB id:
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Hydrolase/hydrolase substrate
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Title:
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The crystal structure of fibrinogen-aa peptide 1-23 (f8y) bound to bovine thrombin explains why the mutation of phe-8 to tyrosine strongly inhibits normal cleavage at arginine-16
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Structure:
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Epsilon thrombin. Chain: l, j. Alpha thrombin. Chain: h. Fibrinopeptide a-alpha. Chain: f, n. Fragment: residues 1 - 23. Engineered: yes. Mutation: yes.
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Source:
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Bos taurus. Cattle. Organism_taxid: 9913. Tissue: blood. Tissue: blood
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Biol. unit:
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Tetramer (from
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Resolution:
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2.50Å
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R-factor:
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0.183
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R-free:
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0.245
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Authors:
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M.G.Malkowski,B.F.P.Edwards
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Key ref:
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M.G.Malkowski
et al.
(1997).
Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16.
Biochem J,
326,
815-822.
PubMed id:
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Date:
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01-May-97
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Release date:
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06-May-98
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PROCHECK
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Headers
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References
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P00735
(THRB_BOVIN) -
Prothrombin from Bos taurus
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Seq:
Struc:
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625 a.a.
29 a.a.
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P00735
(THRB_BOVIN) -
Prothrombin from Bos taurus
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Seq:
Struc:
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625 a.a.
247 a.a.
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Enzyme class:
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Chains L, H, J, K, M:
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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Biochem J
326:815-822
(1997)
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PubMed id:
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Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16.
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M.G.Malkowski,
P.D.Martin,
S.T.Lord,
B.F.Edwards.
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ABSTRACT
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A peptide containing residues 1-50 of the Aalpha-chain of fibrinogen, expressed
as a fusion peptide with beta-galactosidase, is rapidly cleaved by thrombin at
Arg-16, similarly to whole fibrinogen. When Phe-8, which is highly conserved, is
replaced with tyrosine (F8Y), the cleavage is slowed drastically [Lord, Byrd,
Hede, Wei and Colby (1990) J. Biol. Chem. 265, 838-843]. To examine the
structural basis for this result, we have determined the crystal structure of
bovine thrombin complexed with a synthetic peptide containing residues 1-23 of
fibrinogen Aalpha and the F8Y mutation. The crystals are in space group P43212,
with unit-cell dimensions of a = 88.3 A (1 A = 0.1 nm), c = 195.5 A and two
complexes in the asymmetric unit. The final R factor is 0.183 for 2sigma data
from 7.0 to 2.5 A resolution. There is continuous density for the five residues
in the P3, P2, P1, P1' and P2' positions of the peptide (Gly-14f to Pro-18f) at
the active site of thrombin, and isolated but well-defined density for Tyr-8f at
position P9 in the hydrophobic pocket of thrombin. The tyrosine residue is
shifted relative to phenylalanine in the native peptide because the phenol side
chain is larger and makes a novel, intrapeptide hydrogen bond with Gly-14f.
Adjacent peptide residues cannot form the hydrogen bonds that stabilize the
secondary structure of the native peptide. Consequently, the 'reaction'geometry
at the scissile bond, eight residues from the mutation, is perturbed and the
peptide is mostly uncleaved in the crystal structure.
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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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C.Y.Koh,
M.Kazimirova,
P.A.Nuttall,
and
R.M.Kini
(2009).
Noncompetitive inhibitor of thrombin.
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Chembiochem,
10,
2155-2158.
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J.A.Huntington
(2005).
Molecular recognition mechanisms of thrombin.
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J Thromb Haemost,
3,
1861-1872.
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W.Bode
(2005).
The structure of thrombin, a chameleon-like proteinase.
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J Thromb Haemost,
3,
2379-2388.
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K.Ponnuraj,
M.G.Bowden,
S.Davis,
S.Gurusiddappa,
D.Moore,
D.Choe,
Y.Xu,
M.Hook,
and
S.V.Narayana
(2003).
A "dock, lock, and latch" structural model for a staphylococcal adhesin binding to fibrinogen.
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Cell,
115,
217-228.
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PDB codes:
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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.
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Biopolymers,
51,
19-39.
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M.M.Rooney,
J.L.Mullin,
and
S.T.Lord
(1998).
Substitution of tyrosine for phenylalanine in fibrinopeptide A results in preferential thrombin cleavage of fibrinopeptide B from fibrinogen.
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Biochemistry,
37,
13704-13709.
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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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