The refined structure of the .epsilon.-aminocaproic acid complex of human plasminogen kringle 4

Abstract

The crystallographic structure of the plasminogen kringle 4-epsilon-aminocaproic acid (ACA) complex (K4-ACA) has been solved by molecular replacement rotation-translation methods utilizing the refined apo-K4 structure as a search model (Mulichak et al., 1991), and it has been refined to an R value of 0.148 at 2.25-A resolution. The K4-ACA structure consists of two interkringle residues, the kringle along with the ACA ligand, and 106 water molecules. The lysine-binding site has been confirmed to be a relatively open and shallow depression, lined by aromatic rings of Trp62, Phe64, and Trp72, which provide a highly nonpolar environment between doubly charged anionic and cationic centers formed by Asp55/Asp57 and Lys35/Arg71. A zwitterionic ACA ligand molecule is held by hydrogen-bonded ion pair interactions and van der Waals contacts between the charged centers. The lysine-binding site of apo-K4 and K4-ACA have been compared: the rms differences in main-chain and side-chain positions are 0.25 and 0.69 A, respectively, both practically within error of the determinations. The largest deviations in the binding site are due to different crystal packing interactions. Thus, the lysine-binding site appears to be preformed, and lysine binding does not require conformational changes of the host. The results of NMR studies of lysine binding with K4 are correlated with the structure of K4-ACA and agree well.

Lipoprotein (a): truly a direct prothrombotic factor in cardiovascular disease?

“…The LBSs in plasminogen have been shown to be important for both lysine-dependent interactions with substrates, such as fibrin and cell-surface receptors (18)(19)(20), as well as for intramolecular interactions that maintain the closed native conformation of plasminogen (21,22).…”

Comparison of ligand-binding sites of modeled apo[a] kringle-like sequences in human lipoprotein[a].

“…31-33-36 Lysine and analogous molecules such as e-aminocaproic acid occupy most of the available space in the ligand-binding site of PGK4. 36 This can be described as a three-sided pocket, with segments 31-35, 54-57, and 69-72 forming the sides and segment 59-62 forming the base of the pocket. The anionic region, segment 54-57, is formed by Asp54 and Asp56, which interact with the e-amino moiety of the ligand.…”

“…The guanidino group of Arg69 and the e-amino group of Lys35 have been shown to interact with the carboxyl terminus of e-aminocaproic acid ligand. 36 This suggests that either or both cationic moieties may interact with the appropriate carbonyls on a ligand polypeptide main chain. The hydrophobic region, segment 69-72, is formed by Trp70, which forms the trough, or cradle, of the ligandbinding site together with Trp60 of segment 59-62.…”

Structural/functional properties of the Glu1‐HSer57 N‐terminal fragment of human plasminogen: Conformational characterization and interaction with kringle domains

“…1994), computational modeling (Tulinsky et al, 1988), and X-ray crystallography (Wu et al, 1991;de Vos et al, 1992;Mathews et al, 1996). The LBS consists of cationic, anionic, and lipophilic areas that match the electrostatic, hydrophobic, and steric requirements of lysyl-type ligands.…”