 |
PDBsum entry 1j34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Protein binding/blood clotting
|
PDB id
|
|
|
|
1j34
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
129 a.a.
|
|
|
|
|
|
|
|
|
|
|
123 a.a.
|
|
|
|
|
|
|
|
|
|
|
46 a.a.
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Crystal structure of mg2+- And ca2+-Bound gla domain of factor IX complexed with binding protein.
|
|
|
Authors
|
|
Y.Shikamoto,
T.Morita,
Z.Fujimoto,
H.Mizuno.
|
|
|
Ref.
|
|
J Biol Chem, 2003,
278,
24090-24094.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Factor IX is an indispensable protein required in the blood coagulation cascade.
It binds to the surface of phospholipid membrane by means of a
gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we
showed that physiological concentrations of Mg2+ ions affect the native
conformation of the Gla domain and in doing so augment the biological activity
of factor IXa and binding affinity with its binding protein even in the presence
of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound
and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its
binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+
and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions
were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound
with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a
bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative
to IX-bp and hence might be the cause of a more tight interaction between the
molecules than in the case of the Mg2+-free structure. The results clearly
suggest that Mg2+ ions are required to maintain native conformation and in vivo
function of factor IX Gla domain during blood coagulation.
|
|
|
|
|
|
|
|
Figure 1.
FIG. 1. Stereo view of overall structure of the
GD1-46/IX-bp complex. Ribbon model viewed perpendicular to the
pseudodyad of the molecule. The subunits A and B of IX-bp are
magenta and green. IXGD1-46 is in white, and the interchain
disulfide bond is shown in yellow. The bound Mg2^+ and Ca^2^+
ions are drawn as orange and blue spheres, respectively.
|
|
Figure 5.
FIG. 5. Model of factor IXa. The epidermal growth factor
(green) and serine protease (yellow) domains of factor IXa (42)
are shown connected to the IXGD1-46 structure (white), using
factor VIIa structure (17) as a reference model. The bound Mg2^+
and Ca^2^+ ions are drawn as orange and blue spheres,
respectively. D-Phe-Pro-Arg-chloromethylketone, which is bound
to the active site, is shown as a red stick model. The
phospholipid membrane surface is shown by a yellow line.
Hydrophobic residues (yellow), basic residues (purple) and Mg2^+
ion (Mg-1) of GD1-46 are possible candidates for membrane
binding.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
24090-24094)
copyright 2003.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystal structure of an anticoagulant protein in complex with the gla domain of factor x.
|
|
|
Authors
|
|
H.Mizuno,
Z.Fujimoto,
H.Atoda,
T.Morita.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2001,
98,
7230-7234.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Fig. 2. Overall structure of X-bp and XGD1-44 complex.
(A) Stereoview of ribbon model viewed perpendicular to the
pseudodyad of the molecule, showing the interface between X-bp
and XGD1-44. The subunits A and B of X-bp are magenta and green.
XGD1-44 is white. The side chain of Gla residues and disulfide
bonds are displayed. The bound Ca^2+ ions are denoted by blue
spheres. (B) Same view as in A, but molecular detail of
interaction between the hydrophilic patch of XGD1-44 and
positively charged X-bp, and a bridging Ca^2+. (C) Same view as
in B, but between the N terminus hydrophobic patch of XGD1-44
and the C terminus of subunit B of X-bp.
|
|
Figure 3.
Fig. 3. Model of factor Xa bound to X-bp and XGD1-44
bound to membrane. (A) Factor Xa bound to X-bp. The Gla residues
are in red, bound Ca^2+ ions in blue (only labeled is Ca-8,
which is identified in the present study), and disulfide bonds
in green. The small molecule (dark blue) bound to the active
site of the protease domain is the FX-2212a inhibitor (17). (B)
Putative membrane-binding surface of XGD1-44. Same view as in A,
but the scale of the figure is magnified for clarity. The
hydrophobic patch includes Phe4, Leu5, and Val8, and hydrophilic
patch includes Arg28, Gla25, Gla29, Gla32, and Ca-1 as a
bridging Ca^2+, which are on either side of the yellow
horizontal line of the putative membrane surface. Ca-X is a
putative Ca^2+ ion that is taken in as another bridging Ca^2+.
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Crystal structure of coagulation factor IX-Binding protein from habu snake venom at 2.6 a: implication of central loop swapping based on deletion in the linker region.
|
|
|
Authors
|
|
H.Mizuno,
Z.Fujimoto,
M.Koizumi,
H.Kano,
H.Atoda,
T.Morita.
|
|
|
Ref.
|
|
J Mol Biol, 1999,
289,
103-112.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 5.
Figure 5. Geometry around the Ca
2+
-binding sites: (a) subunit A; (b) subunit B. White, blue and red lines show car-
bon, nitrogen and oxygen atoms, respectively.
|
|
Figure 6.
Figure 6. Comparison of hydrophobic interactions in the C-interfaces between IX-bp (top) and MBP (bottom).
Asn76 to Ala91 in the CLR of subunit B interacts with amino acid residues in the body of subunit A (pink) in IX-bp.
In MBP, Gln167 to Lys182 in the CLR interacts with amino acid residues in the body (pink). Amino acid residues par-
ticipating in the hydrophobic interactions are labeled.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from Elsevier
|
|
|
|
|
|
|
