Structural basis for chemical inhibition of human blood coagulation factor Xa

Kamata, Kenji; Kawamoto, Hiroshi; Honma, Teruki; Iwama, Toshiharu; Kim, Sung‐Hou

doi:10.1073/pnas.95.12.6630

Cited by 133 publications

(118 citation statements)

References 46 publications

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“…1a). The EGF2 domain and the protease domain associate into the compact structural unit that is common to factors VIIa (6), IXa (18), and Xa (19)(20)(21) and to activated protein C (22). The first EGF-like domain (EGF1) extends away from this compact core at an angle of 120°to yield a molecule with a linear length of Ϸ90 Å.…”

Section: Resultsmentioning

confidence: 99%

Structure of human factor VIIa and its implications for the triggering of blood coagulation

Pike

Brzozowski

Roberts

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

148

123

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Factor VIIa (EC 3.4.21.21) is a trypsin-like serine protease that plays a key role in the blood coagulation cascade. On injury, factor VIIa forms a complex with its allosteric regulator, tissue factor, and initiates blood clotting. More importantly, a surface-exposed ␣-helix in the protease domain (residues 307-312), which is located at the cofactor recognition site, is distorted in the free form of factor VIIa. This subtle structural difference sheds light on the mechanism of the dramatic tissue factor-induced enhancement of factor VIIa activity.

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Section: Resultsmentioning

confidence: 99%

Structure of human factor VIIa and its implications for the triggering of blood coagulation

Pike

Brzozowski

Roberts

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

148

123

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“…The two cassette modules of the light chain show strong sequence and structural homology to epidermal growth factor (EGF) (4) and are thus referred to as EGF N and EGF C , where N and C indicate the domain nearer to the N and C termini, respectively. Crystal structures of Gla domain-less factor X a (GDFX a ) have been published (5)(6)(7). In the most recent of these (7), the EGF cassette modules extend from the catalytic domain to make an extended molecule.…”

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confidence: 99%

“…Crystal structures of Gla domain-less factor X a (GDFX a ) have been published (5)(6)(7). In the most recent of these (7), the EGF cassette modules extend from the catalytic domain to make an extended molecule. In the structure of the analogous serine protease, factor IX a , the EGF N module is bent at the inner-EGF C hinge region to right angles with the EGF C , which is tucked along the catalytic module (8).…”

mentioning

confidence: 99%

Localization of Phosphatidylserine Binding Sites to Structural Domains of Factor Xa

Srivastava¹,

Wang²,

Majumder³

et al. 2002

Journal of Biological Chemistry

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Binding of short chain phosphatidylserine (C6PS) enhances the proteolytic activity of factor X a by 60-fold (Koppaka, V., Wang, J., Banerjee, M., and Lentz, B. R. (1996) Biochemistry 35, 7482-7491). In the present study, we locate three C6PS binding sites to different domains of factor X a using a combination of activity, circular dichroism, fluorescence, and equilibrium dialysis measurements on proteolytic and biosynthetic fragments of factor X a . Our results demonstrate that the structural responses of human and bovine factor X a to C6PS binding are somewhat different. Despite this difference, data obtained with fragments from both human and bovine factor X a are consistent with a common hypothesis for the location of C6PS binding sites to different structural domains. First, the ␥-carboxyglutamic acid (Gla) domain binds C6PS only in the absence of Ca 2؉ (k d ϳ 1 mM), although this PS site does not influence the functional response of factor X a . Second, a Ca 2؉ -dependent binding site is in the epidermal growth factor domains (EGF NC ) that are linked by Ca 2؉ and C6PS binding to the Gla domain. This site appears to be the lipid regulatory site of factor X a . Third, a Ca 2؉ -requiring site seems to be in the EGF C -catalytic domain. This site appears not to be a lipid regulatory site but rather to share residues with the substrate recognition site. Finally, the full functional response to C6PS requires linkage of the Gla, EGF NC , and catalytic domains in the presence of Ca 2؉ , meaning that PS regulation of factor X a involves linkage between widely separated parts of the protein.The substantial effects of soluble phosphatidylserine (C6PS 1 ) on the kinetics of prothrombin activation by factor X a(1) and on the structure of factor X a , as documented here, indicate that phosphatidylserine (PS) may act as an allosteric regulator of prothrombin activation. PS located on the cytoplasmic face of resting platelet plasma membranes is exposed on the surface of activated platelet vesicles (2, 3). The implication of this PS exposure and of the effect of PS on factor X a and on its ability to catalyze activation of prothrombin is that PS may act as a second messenger in regulating thrombin formation. Because of the crucial role of thrombin in hemostasis, the exposure of PS may be a crucial regulatory step in blood coagulation. To better define this regulatory process, it is important to know the locations of the PS binding sites on factor X a . The organization of factor X into structural domains is illustrated below in Fig. 1. Factor X consists of two peptides. The light chain consists of an N terminus ␥-carboxyglutamic acidrich region (Gla module) and two Cys-rich cassette modules. The heavy chain consists of the serine protease catalytic domain. The two cassette modules of the light chain show strong sequence and structural homology to epidermal growth factor (EGF) (4) and are thus referred to as EGF N and EGF C , where N and C indicate the domain nearer to the N and C termini, respectively. Crystal structures o...

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“…Two different schemes were adopted to construct the homology model for PZ: one using multiple sequence alignment of human FVIIa [13], FIXa [14], FXa [15] and PC [16] sequences, and the other using FVIIa as a single template (see supplementary Fig. S1 for the sequence alignment).…”

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confidence: 99%

A proposed structural model of human protein Z

Lee

Chandrasekaran

Duke

et al. 2007

Journal of Thrombosis and Haemostasis

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Analysis of structures and sequence similarities of the vitamin K-dependent (VKD) proteins in the blood coagulation pathway has shown that these proteins have evolved through a series of gene duplications and diversification, acquiring a degree of functional diversity in the process [1][2][3]. Protein Z (PZ) is a VKD plasma glycoprotein that is highly conserved across different species. It is homologous to the blood coagulation factors VII (FVII), FIX, FX, and protein C (PC). However, PZ differs from other coagulation proteins in that it lacks the critical histidine and serine residues of the catalytic triad, and is therefore not a zymogen of a serine protease (SP) [4,5].Human PZ was first isolated in 1984 [6], and its gene was characterized in 1998 [7]. PZ is relatively abundant in humans, with a wide plasma concentration range, and circulates as a complex with PZ-dependent protease inhibitor (ZPI) [8][9][10]. It has been shown to function as a cofactor in the inhibition of activated FX (FXa) by ZPI, causing a thousandfold increase in inhibition in a Ca 2+ -dependent manner [11]. The relative abundance in plasma and sequence similarity with other VKD proteins serve to pique our interest in the PZ system.In order to gain a better understanding of the function and evolutionary significance of PZ, it is important to start from structural information at an atomic level. Although PZ was isolated over 20 years ago, its physiologic role in relation to its molecular structure is still not clear. In this study, we propose a solvent-equilibrated structural model of human PZ using homology modeling and molecular dynamics (MD) simulation. The possibility of using this approach is supported by recent findings [12].Human PZ is a single-chain molecule of 360 residues with four domains: a Gla domain (residues 1-46) with 13 ccarboxyglutamic acid (Gla) residues (residues 7, 8, 11, 15, 17, 20, 21, 26, 27, 30, 33, 35 and 40), two epidermal growth factor (EGF)-like domains -an EGF1 domain (residues 47-83) with a b-hydroxyaspartate (Bha) residue at 64, and an EGF2 domain (residues 85-126) -and an SP-like domain (residues 135-360) with high homology to the catalytic domain of other VKD SPs [4,5].We have employed an iterative process of homology modeling and structure evaluation followed by MD simulation to construct a solvent-equilibrated structural model of PZ. Two different schemes were adopted to construct the homology model for PZ: one using multiple sequence alignment of human FVIIa [13] 18-23, 51-62, 56-71, 73-82, 89-101, 97-110, 112-125, 163-179 and 287-301). To obtain a refined solvent-equilibrated model and to remove bad contacts in the homology model, we performed an MD simulation using PMEMD9 in the AMBER9 [20] suite with the ff99SB forcefield. The total system was composed of 99 459 atoms, including 12 calcium ions, four sodium counterions for neutralizing the system, and 31 307 TIP3P water molecules. The seven conserved calcium ions in the Gla domain were placed on the basis of FVIIa, and the additional calcium ions w...

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Structural basis for chemical inhibition of human blood coagulation factor Xa

Cited by 133 publications

References 46 publications

Structure of human factor VIIa and its implications for the triggering of blood coagulation

Structure of human factor VIIa and its implications for the triggering of blood coagulation

Localization of Phosphatidylserine Binding Sites to Structural Domains of Factor Xa

A proposed structural model of human protein Z

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