A Three-Dimensional Model of Human Lysyl Oxidase, a Cross-Linking Enzyme

Abstract

Lysyl oxidase (LOX) is a cross-linking enzyme identified 50 years ago, but its 3D structure is still unknown. We have thus built a 3D model of human LOX by homology modeling using the X-ray structure of human lysyl oxidase-like 2 as a template. This model is the first one to recapitulate all known biochemical features of LOX, namely, the coordination of the copper ion and the formation of the lysine tyrosylquinone cofactor and the disulfide bridges. Furthermore, this model is stable during a 1 μs molecular dynamics simulation. The catalytic site is located in a groove surrounded by two loops. The distance between these loops fluctuated during the simulations, which suggests that the groove forms a hinge with a variable opening, which is able to accommodate the various sizes of LOX substrates. This 3D model is a pre-requisite to perform docking experiments with LOX substrates and other partners to identify binding sites and to design new LOX inhibitors specific for therapeutic purpose.

Lysyl Oxidase Like‐2 (LOXL2): An Emerging Oncology Target

“…The crystal structure of LOXL2 in its functional state (with LTQ cofactor) has to date eluded solution . This precursor crystal structure of LOXL2 has, however, assisted in generating a 3D model for the LOX family …”

“…crystal structure of LOXL2 has, however, assisted in generating a 3D model for the LOX family. [24,25] The LTQ region in LOXL2 is defined by the residues Y689 and K653 ( Figure 3). [22] The primary role of LOX enzymes is to catalyze the oxidative deamination of lysine and hydroxylysine residues in collagen and elastin of the extracellular matrix (ECM).…”

Lysyl Oxidase (LOX): Functional Contributions to Signaling Pathways

“…A recent three dimensional (3-D) model of LOX generated by homology modeling recaptured the essential domains, the coordination of the Cu ion, the lysyl tyrosylquinone LTQ cofactor, disulfide bridges and the catalytic site within a groove surrounded by two fluctuating loops with variable openings which are suitable for the accommodation of LOX substances of different sizes [ 8 ]. LOX also participates in various activity-independent functions, the mechanistic details of which remain to be fully characterized.…”

The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins

“…The interactome reported here is enriched in LOXL4 partners (91) compared to the previously reported LOXL4 interactome, which contained 15 partners [ 34 ]. To further increase the coverage of the LOX family interactome, ECM calcium-binding proteins could be assayed for their binding to LOX and LOXLs because a calcium-binding site has been found in the 3D structure of a precursor of human LOXL2 [ 55 ], and we have shown that this site is conserved in the 3D model of human LOX [ 56 ]. The 2-fold enrichment in exosomes in the LOX family interactome suggests that ECM cross-linking by hypoxic endothelial cell-derived exosomes mediated by LOXL2 [ 57 ], and exosome-mediated secretion of LOXL4 promoting hepatocellular carcinoma cell invasion and metastasis [ 15 ] might involve other members of the family and their partners.…”

“…The 2-fold enrichment in exosomes in the LOX family interactome suggests that ECM cross-linking by hypoxic endothelial cell-derived exosomes mediated by LOXL2 [ 57 ], and exosome-mediated secretion of LOXL4 promoting hepatocellular carcinoma cell invasion and metastasis [ 15 ] might involve other members of the family and their partners. The three-dimensional model of LOX we have recently built [ 56 ], and the crystal structure of a precursor state of LOXL2 [ 55 ], could be used for docking experiments to map the binding sites of their partners, and predict those which could be either substrates or modulators of LOX and LOXL enzyme activity by binding to their catalytic sites. These potential substrates will then be tested in vitro to determine if they are modified by LOX and LOXL2, or if they regulate their enzymatic activity.…”