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Solution structure of the smallest cofactor-active fragment of thrombomodulin

Nature Structural Biology volume 7, pages 200–204 (2000)Cite this article

Abstract

A glycosylated fragment of thrombomodulin containing two epidermal growth factor-like domains (TMEGF45) was analyzed by NMR. The 4th-domains structure of this two-domain fragment is similar to that of the individual domain previously determined. The 5th-domain, which has uncrossed disulfide bonds, is not as well determined in the two-domain fragment than the individual domain previously solved. The flexibility of the 5th-domain is consistent with low heteronuclear NOEs. In the individual 5th-domain, Met 388 was disordered, and key thrombin-binding residues formed a hydrophobic core. By contrast, in TMEGF45, Met 388 is in the 5th-domain core, positioned by Phe 376 from the 4th-domain. As a result, key thrombin-binding residues that were in the core of the individual domain are expelled. Upon thrombin binding, chemical shifts of two residues in the 4th-domain, the three interdomain linker residues, and nearly all of the 5th-domain are perturbed. Thus, TMEGF45 binds thrombin by an induced fit mechanism involving a flexible 5th-domain.

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Figure 1: NMR data for TMEGF45.
Figure 2: Structure of TMEGF45.
Figure 3: Analysis of TMEGF45 structure.
Figure 4: Central role of Met 388 in interdomain contacts.

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  1. Department of Chemistry and Biochemistry, University of California, 9500 Gilman Dr., San Diego, La Jolla, 92093-0359, California, USA

    Matthew J. Wood, Benedetta A. Sampoli Benitez & Elizabeth A. Komives

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  1. Matthew J. Wood
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  2. Benedetta A. Sampoli Benitez
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  3. Elizabeth A. Komives
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Correspondence to Elizabeth A. Komives.

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Wood, M., Sampoli Benitez, B. & Komives, E. Solution structure of the smallest cofactor-active fragment of thrombomodulin. Nat Struct Mol Biol 7, 200–204 (2000). https://doi.org/10.1038/73302

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