Crystal structure of the kringle 2 domain of tissue plasminogen activator at 2.4-A resolution.de Vos, A.M., Ultsch, M.H., Kelley, R.F., Padmanabhan, K., Tulinsky, A., Westbrook, M.L., Kossiakoff, A.A.
(1992) Biochemistry 31: 270-279
- PubMed: 1310033
- DOI: https://doi.org/10.1021/bi00116a037
- Primary Citation of Related Structures:
- PubMed Abstract:
The crystal structure of the kringle 2 domain of tissue plasminogen activator was determined and refined at a resolution of 2.43 A. The overall fold of the molecule is similar to that of prothrombin kringle 1 and plasminogen kringle 4; however, there are differences in the lysine binding pocket, and two looping regions, which include insertions in kringle 2, take on very different conformations. Based on a comparison of the overall structural homology between kringle 2 and kringle 4, a new sequence alignment for kringle domains is proposed that results in a division of kringle domains into two groups, consistent with their proposed evolutionary relation. The crystal structure shows a strong interaction between a lysine residue of one molecule and the lysine/fibrin binding pocket of a noncrystallographically related neighbor. This interaction represents a good model of a bound protein ligand and is the first such ligand that has been observed in a kringle binding pocket. The structure shows an intricate network of interactions both among the binding pocket residues and between binding pocket residues and the lysine ligand. A lysine side chain is identified as the positively charged group positioned to interact with the carboxylate of lysine and lysine analogue ligands. In addition, a chloride ion is located in the kringle-kringle interface and contributes to the observed interaction between kringle molecules.
Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.