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Supplementary information for Structure 5(1): 125 - 138 (1997)
Welcome to the world of coagulation factors
Most of us have cut ourselves at one time or another. Think of the process that occurs when this happens. First it bleeds a bit, followed by a soft clot forming and later some plasma may squeeze through the clot as it "matures". Finally a scab forms and the wound heals.
Many marvelous chemical reactions occur in this process. The coagulation cascade is triggered. This cascade was first elucidated by Earl W. Davie & coworkers of the U.W. Department of Biochemistry, and consists of about 15 enzyme reactions wherein each enzyme activates an inactive precursor (zymogen) to form an active enzyme. The process is rather similar to a pre-amplifier on a phonograph player. In the final steps of this cascade, the enzyme thrombin (factor IIa) activates factor XIII to factor XIIIa and at the same time removes peptides from fibrinogen creating fibrin. In the activation of factor XIII, fibrin serves as a cofactor facilitating a structural change in the enzyme.
Fibrin polymerizes spontaneously to form a fibril and the catalytic activity of factor XIII comes into play. Factor XIIIa catalyzes the formation of glutamyl-lysyl crosslinks between the adjacent fibrin molecules, stabilizing the blood clot. In addition, factor XIIIa catalyzes the formation of crosslinks between fibrin and alpha-2-antiplasmin, an inhibitor of plasmin, the enzyme which catalyzes clot digestion. In this way, the clot insures it will not be immediately digested away. In addition to all of these reactions, factor XIIIa catalyzes the formation of crosslinks to the tissue substrate to hold the clot in place. By mechanisms which are currently unknown, but probably linked to calcium concentrations, the fibrin clot spontaneously shrinks after crosslinking, closing the wound.
As might be imagined there are many controls of coagulation. When a clot forms, it does not continue indefinitely but is confined to the site of the injury. Several of the control proteins are known at present, but almost certainly some remain to be discovered.
Factor XIII is a member of a larger family of transglutaminases. At the present time sequences of 20 of these proteins have been determined and all are closely related to factor XIII (35 to 55 percent amino acid sequence identity). A careful comparison of the structure of factor XIII with Papain (a representative member of the cysteine proteinase family) has revealed that the central core of the enzyme structure as well as the catalytic apparatus is so similar as to indicate divergent evolution from a common ancestral protein. This similarity has allowed us to postulate the catalytic mechanism of the reaction with considerable confidence.
Many questions and problems concerning this fascinating protein remain to be solved. We have yet to determine the structure of an enzyme form poised for catalysis. We also do not know the binding sites for the glutamyl and lysyl substrates. The two C-terminal domains of the protein are topologically similar to fibronectin type III domains but bear no sequence resemblance to the fibronectin domains. Are these domains involved in substrate specificity? Finally, how does binding to fibrin by the enzyme or zymogen facilitate the structural changes necessary for catalysis?
The human blood coagulation
A-subunit dimer structure, as determined by our X-ray
crystallography efforts. Each subunit contains 730 amino acid residues
and the total formula weight is 166,000 daltons. Factor XIII is a
calcium-dependent transglutaminase and covalently crosslinks blood clots
in the final stage of the coagulation process.
Occasionally folks who "visit" this web page wish to learn more about the clinical aspects of factor XIII deficiency. One may wish to consult the following reference in "Seminars in Thrombosis and Hemostasis", Volume 22, Number 5 pp 367-456 (1996). This issue contains a variety of papers presented in Marburg, Germany in June 1995. The title of the proceedings is "Factor XIII: state of the art 1996" edited by R. Seitz, J. McDonagh, and R. Egbring. The journal (Seminars in Thrombosis and Hemostasis) should be available in the medical school of your local university.
We were recently able to determine the structure of a 30 kDa fragment of the gamma chain of human fibrinogen. The reference for this research is V.C.Yee, et al, Structure 5(1): 125 - 138 (1997). Supplementary information for that manuscript is presented in a separate file.
David C. Teller
The Biomolecular Structure Center at UW