The 2.8 A Crystal Structure of Gla-domainless Activated Protein C

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 1996 Dec 16

PMID 9003757

Citations 71

Authors

T Mather

V Oganessyan

P Hof

R Huber

S Foundling

C Esmon

W Bode

Affiliations

Soon will be listed here.

Abstract

The structure of the Gla-domainless form of the human anticoagulant enzyme activated protein C has been solved at 2.8 A resolution. The light chain is composed of two domains: an epidermal growth factor (EGF)-like domain modified by a large insert containing an additional disulfide, followed by a typical EGF-like domain. The arrangement of the long axis of these domains describes an angle of approximately 80 degrees. Disulfide linked to the light chain is the catalytic domain, which is generally trypsin-like but contains a large insertion loop at the edge of the active site, a third helical segment, a prominent cationic patch analogous to the anion binding exosite I of thrombin and a trypsin-like Ca[II] binding site. The arrangement of loops around the active site partially restricts access to the cleft. The S2 and S4 subsites are much more polar than in factor Xa and thrombin, and the S2 site is unrestricted. While quite open and exposed, the active site contains a prominent groove, the surface of which is very polar with evidence for binding sites on the primed side, in addition to those typical of the trypsin class found on the non-primed side.

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References

Grinnell B, Hermann R, Yan S . Human protein C inhibits selectin-mediated cell adhesion: role of unique fucosylated oligosaccharide. Glycobiology. 1994; 4(2):221-5. DOI: 10.1093/glycob/4.2.221. View

Guinto E, Ye J, Le Bonniec B, Esmon C . Glu192-->Gln substitution in thrombin yields an enzyme that is effectively inhibited by bovine pancreatic trypsin inhibitor and tissue factor pathway inhibitor. J Biol Chem. 1994; 269(28):18395-400. View

Kalafatis M, Rand M, Mann K . The mechanism of inactivation of human factor V and human factor Va by activated protein C. J Biol Chem. 1994; 269(50):31869-80. View

Rivard G, David M, Farrell C, Schwarz H . Treatment of purpura fulminans in meningococcemia with protein C concentrate. J Pediatr. 1995; 126(4):646-52. DOI: 10.1016/s0022-3476(95)70369-1. View

Vijayalakshmi J, Padmanabhan K, Mann K, Tulinsky A . The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin. Protein Sci. 1994; 3(12):2254-71. PMC: 2142772. DOI: 10.1002/pro.5560031211. View

Rezaie A, Esmon C . Contribution of residue 192 in factor Xa to enzyme specificity and function. J Biol Chem. 1995; 270(27):16176-81. DOI: 10.1074/jbc.270.27.16176. View

Neuenschwander P, Morrissey J . Alteration of the substrate and inhibitor specificities of blood coagulation factor VIIa: importance of amino acid residue K192. Biochemistry. 1995; 34(27):8701-7. DOI: 10.1021/bi00027a020. View

Esmon C . Thrombomodulin as a model of molecular mechanisms that modulate protease specificity and function at the vessel surface. FASEB J. 1995; 9(10):946-55. DOI: 10.1096/fasebj.9.10.7615164. View

Dahlback B . Thrombophilia: the discovery of activated protein C resistance. Adv Genet. 1995; 33:135-75. DOI: 10.1016/s0065-2660(08)60333-8. View

10.

Brandstetter H, Bauer M, Huber R, Lollar P, Bode W . X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B. Proc Natl Acad Sci U S A. 1995; 92(21):9796-800. PMC: 40889. DOI: 10.1073/pnas.92.21.9796. View

11.

Rezaie A, Esmon C . Tryptophans 231 and 234 in protein C report the Ca(2+)-dependent conformational change required for activation by the thrombin-thrombomodulin complex. Biochemistry. 1995; 34(38):12221-6. DOI: 10.1021/bi00038a016. View

12.

Reitsma P, Bernardi F, Doig R, Gandrille S, Greengard J, Ireland H . Protein C deficiency: a database of mutations, 1995 update. On behalf of the Subcommittee on Plasma Coagulation Inhibitors of the Scientific and Standardization Committee of the ISTH. Thromb Haemost. 1995; 73(5):876-89. View

13.

MAMMEN E, Thomas W, SEEGERS W . Activation of purified prothrombin to autoprothrombin I or autoprothrombin II (platelet cofactor II or autoprothrombin II-A). Thromb Diath Haemorrh. 1960; 5:218-49. View

14.

Schechter I, Berger A . On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun. 1967; 27(2):157-62. DOI: 10.1016/s0006-291x(67)80055-x. View

15.

Bode W, Schwager P . The refined crystal structure of bovine beta-trypsin at 1.8 A resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0. J Mol Biol. 1975; 98(4):693-717. DOI: 10.1016/s0022-2836(75)80005-2. View

16.

Stenflo J . A new vitamin K-dependent protein. Purification from bovine plasma and preliminary characterization. J Biol Chem. 1976; 251(2):355-63. View

17.

SEEGERS W, Novoa E, Henry R, Hassouna H . Relationship of "new" vitamin K-dependent Protein C and "old" autoprothrombin II-a. Thromb Res. 1976; 8(5):543-52. DOI: 10.1016/0049-3848(76)90236-x. View

18.

Comp P, Esmon C . Generation of fibrinolytic activity by infusion of activated protein C into dogs. J Clin Invest. 1981; 68(5):1221-8. PMC: 370917. DOI: 10.1172/jci110368. View

19.

Griffith M . Kinetics of the heparin-enhanced antithrombin III/thrombin reaction. Evidence for a template model for the mechanism of action of heparin. J Biol Chem. 1982; 257(13):7360-5. View

20.

Fernlund P, Stenflo J . Amino acid sequence of the light chain of bovine protein C. J Biol Chem. 1982; 257(20):12170-9. View