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PDBsum entry 1ixa
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Human factor ix
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PDB id
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1ixa
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.22
- coagulation factor IXa.
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Reaction:
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Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.
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DOI no:
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Protein Sci
1:81-90
(1992)
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PubMed id:
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The three-dimensional structure of the first EGF-like module of human factor IX: comparison with EGF and TGF-alpha.
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M.Baron,
D.G.Norman,
T.S.Harvey,
P.A.Handford,
M.Mayhew,
A.G.Tse,
G.G.Brownlee,
I.D.Campbell.
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ABSTRACT
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The three-dimensional structure of the first epidermal growth factor (EGF)-like
module from human factor IX has been determined in solution using
two-dimensional nuclear magnetic resonance (in the absence of calcium and at pH
4.5). The structure was found to resemble closely that of EGF and the homologous
transforming growth factor-alpha (TGF-alpha). Residues 60-65 form an
antiparallel beta-sheet with residues 68-73. In the C-terminal subdomain a type
II beta-turn is found between residues 74 and 77 and a five-residue turn is
found between residues 79 and 83. Glu 78 and Leu 84 pair in an antiparallel
beta-sheet conformation. In the N-terminal region a loop is found between
residues 50 and 55 such that the side chains of both are positioned above the
face of the beta-sheet. Residues 56-60 form a turn that leads into the first
strand of the beta-sheet. Whereas the global fold closely resembles that of EGF,
the N-terminal residues of the module (46-49) do not form a beta-strand but are
ill-defined in the structure, probably due to the local flexibility of this
region. The structure is discussed with reference to recent site-directed
mutagenesis data, which have identified certain conserved residues as ligands
for calcium.
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Selected figure(s)
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Figure 2.
Fig. 2. Experimentalrestraints. A: Experimentaldata used to identifysecondarystructure. Black boxesrepresentHN,HN<,,i-,,
andHN,Ha(,,,-,,NOEs.Theheightoftheboxrelatestothe size oftheNOE(strong,medium,weak).Openboxesrepresent
NOEs romprolineH6protons. S ndicatesresidueswhosebackboeaideprotonswere slow to xchange in D20, ad * in-
icates 3JHN ouplingconstantsgreaterthan 9 Hz. B: Thedistribution f long-range andshort-rangedistancerestraints.
barsrepresentlong-rangedistancerestraints(>i - [i + 1); openbarsrepresentshort-rangedistancerestraints(
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Figure 3.
Fig. 3. Distribution of NOE restraint energy forstructures produced
by restrained simulated annealing (i.e., prior o final minimization). Re-
straint energies are in kJ/mol; selection cutoff at 369 kJ/mol, denoted
by a
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1992,
1,
81-90)
copyright 1992.
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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
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J.C.Adams
(2001).
Thrombospondins: multifunctional regulators of cell interactions.
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Annu Rev Cell Dev Biol,
17,
25-51.
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C.Valcarce,
I.Björk,
and
J.Stenflo
(1999).
The epidermal growth factor precursor. A calcium-binding, beta-hydroxyasparagine containing modular protein present on the surface of platelets.
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Eur J Biochem,
260,
200-207.
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Y.H.Kao,
G.F.Lee,
Y.Wang,
M.A.Starovasnik,
R.F.Kelley,
M.W.Spellman,
and
L.Lerner
(1999).
The effect of O-fucosylation on the first EGF-like domain from human blood coagulation factor VII.
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Biochemistry,
38,
7097-7110.
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PDB codes:
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A.W.Ashton,
M.K.Boehm,
D.J.Johnson,
G.Kemball-Cook,
and
S.J.Perkins
(1998).
The solution structure of human coagulation factor VIIa in its complex with tissue factor is similar to free factor VIIa: a study of a heterodimeric receptor-ligand complex by X-ray and neutron scattering and computational modeling.
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Biochemistry,
37,
8208-8217.
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B.Bersch,
J.F.Hernandez,
D.Marion,
and
G.J.Arlaud
(1998).
Solution structure of the epidermal growth factor (EGF)-like module of human complement protease C1r, an atypical member of the EGF family.
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Biochemistry,
37,
1204-1214.
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PDB code:
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D.Tolkatchev,
and
F.Ni
(1998).
Calcium binding properties of an epidermal growth factor-like domain from human thrombomodulin.
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Biochemistry,
37,
9091-9100.
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M.Lohmeyer,
P.M.Harrison,
S.Kannan,
M.DeSantis,
N.J.O'Reilly,
M.J.Sternberg,
D.S.Salomon,
and
W.J.Gullick
(1997).
Chemical synthesis, structural modeling, and biological activity of the epidermal growth factor-like domain of human cripto.
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Biochemistry,
36,
3837-3845.
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C.E.White,
M.J.Hunter,
D.P.Meininger,
S.Garrod,
and
E.A.Komives
(1996).
The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern.
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Proc Natl Acad Sci U S A,
93,
10177-10182.
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J.Hvarregaard,
M.H.Andersen,
L.Berglund,
J.T.Rasmussen,
and
T.E.Petersen
(1996).
Characterization of glycoprotein PAS-6/7 from membranes of bovine milk fat globules.
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Eur J Biochem,
240,
628-636.
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R.Tejero,
D.Bassolino-Klimas,
R.E.Bruccoleri,
and
G.T.Montelione
(1996).
Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.
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Protein Sci,
5,
578-592.
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S.J.Freedman,
D.G.Sanford,
W.W.Bachovchin,
B.C.Furie,
J.D.Baleja,
and
B.Furie
(1996).
Structure and function of the epidermal growth factor domain of P-selectin.
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Biochemistry,
35,
13733-13744.
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PDB code:
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D.P.Meininger,
M.J.Hunter,
and
E.A.Komives
(1995).
Synthesis, activity, and preliminary structure of the fourth EGF-like domain of thrombomodulin.
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Protein Sci,
4,
1683-1695.
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PDB code:
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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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D.Zhong,
K.J.Smith,
J.J.Birktoft,
and
S.P.Bajaj
(1994).
First epidermal growth factor-like domain of human blood coagulation factor IX is required for its activation by factor VIIa/tissue factor but not by factor XIa.
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Proc Natl Acad Sci U S A,
91,
3574-3578.
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M.Tartary,
D.Vidaud,
Y.Piao,
J.M.Costa,
B.R.Bahnak,
E.Fressinaud,
B.Congard,
Y.Laurian,
D.Meyer,
and
J.M.Lavergne
(1993).
Detection of a molecular defect in 40 of 44 patients with haemophilia B by PCR and denaturing gradient gel electrophoresis.
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Br J Haematol,
84,
662-669.
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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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