High resolution structure of human apolipoprotein (a) kringle IV type 2: beyond the lysine binding site

Abstract

Lipoprotein (a) [Lp(a)] is characterized by an LDL-like composition in terms of lipids and apoB100, and by one copy of a unique glycoprotein, apolipoprotein (a) [apo(a)]. The apo(a) structure is mainly based on the repetition of tandem kringle domains with high homology to plasminogen kringles 4 and 5. Among them, kringle IV type 2 (KIV-2) is present in a highly variable number of genetically encoded repeats, whose length is inversely related to Lp(a) plasma concentration and cardiovascular risk. Despite it being the major component of apo(a), the actual function of KIV-2 is still unclear. Here, we describe the first high-resolution crystallographic structure of this domain. It shows a general fold very similar to other KIV domains with high and intermediate affinity for the lysine analogue ε-aminocaproic acid (EACA). Interestingly, KIV-2 presents a Lysine Binding Site (LBS) with a unique shape and charge distribution. KIV-2 affinity for predicted small molecule binders was found to be negligible in Surface Plasmon Resonance (SPR) experiments, and with the LBS being nonfunctional, we propose to rename it “pseudo-LBS” (pLBS). Further investigation of the protein by computational small-molecule docking allowed us to identify a possible heparin-binding site away from the LBS, which was confirmed by specific reverse charge mutations abolishing heparin binding. This study opens new possibilities to define the pathogenesis of Lp(a) related diseases and to facilitate the design of specific therapeutic drugs. (226 words)

Haplotype of the Lipoprotein(a) Gene Variants rs10455872 and rs3798220 Is Associated with Parameters of Coagulation, Fibrinolysis, and Inflammation in Patients after Myocardial Infarction and Highly Elevated Lipoprotein(a) Values

“…Even more important is our finding that OFP was related to the number of KIV-2 repeats. The number of KIV-2 repeats not only is related to Lp(a) concentration, as we also showed in our research, but also determines the structure of apo(a) [35]. The number of KIV-2 repeats thus affects not only the concentration of Lp(a), and thus its proatherosclerotic and proinflammatory effects, but also the structure of apo(a) and its associated antifibrinolytic properties.…”

Crystal structure of the kringle domain of human receptor tyrosine kinase-like orphan receptor 1 (hROR1)

“…4a). In particular, hROR1-KRD showed strong similarity to the K1 domain of hepatocyte growth factor (HGF/SF; Sigurdardottir et al, 2015), KIV domains 2, 7 and 10 of human apolipoprotein A (Ye et al, 2001;Santonastaso et al, 2020;Mochalkin et al, 1999), KRD2 and KRD4 of human plasminogen (PDB entries 6oqk and 1krn; Yuan et al, 2019;Stec et al, 1997), KRD1 of prothrombin (Huang et al, 2003) and the KRD of neurotrypsin (PDB entry 2k51; Ozhogina et al, 2008) (Supplementary Table S1).…”

Lipoprotein(a) and Atherosclerotic Cardiovascular Disease: Where Do We Stand?

“…While plasminogen contains five kringle domains (KI, KII, KIII, KIV, and KV) and one protease domain, apo(a) consists of a single kringle V domain (KV), ten different types of kringle IV domains (KIV1 to KIV10), and a catalytically inactive protease domain at the carboxyl terminus [ 13 ]. The size heterogeneity of apo(a) is determined by the variable number of KIV2 domain copies, which can range from 1 to over 40, while the remaining KIV domains are typically present as single copies [ 14 , 15 ]. Figure 1 provides a schematic presentation of the structure of the Lp(a) particle.…”