title: Crystal structure of the kringle 2 domain of tissue plasminogen activator at 2.4-A resolution.
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.
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080.
authors.forename: A M
authors.initials: AM
authors.lastname: de Vos
authors.forename: M H
authors.initials: MH
authors.lastname: Ultsch
authors.forename: R F
authors.initials: RF
authors.lastname: Kelley
authors.forename: K
authors.initials: K
authors.lastname: Padmanabhan
authors.forename: A
authors.initials: A
authors.lastname: Tulinsky
authors.forename: M L
authors.initials: ML
authors.lastname: Westbrook
authors.forename: A A
authors.initials: AA
authors.lastname: Kossiakoff
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D005341:Fibrinolysin / Q000737:chemistry; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010316:Particle Size; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D012689:Sequence Homology, Nucleic Acid; D013237:Stereoisomerism; D010959:Tissue Plasminogen Activator / Q000737:chemistry* / Q000235:genetics; D014961:X-Ray Diffraction
chemical_list: D010446:Peptide Fragments; D010959:Tissue Plasminogen Activator; D005341:Fibrinolysin; D008239:Lysine