Lipoxygenase iron-binding catalytic domain signatures and profile

Lipoxygenases (EC 1.13.11.-) are a class of iron-containing dioxygenases which catalyzes the hydroperoxidation of lipids, containing a cis,cis-1,4-pentadiene structure. The primary products are hydroperoxy fatty acids, which usually are rapidly reduced to hydroxy derivatives. Lipoxygenases are common in plants where they may be involved in a number of diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding [1]. In mammals a number of lipoxygenases isozymes are involved in the metabolism of prostaglandins and leukotrienes [2]. Lipoxygenases are also common in primitive animals such as coral [3] and occur in some bacteria [4,5]. The N-terminal part of the eukaryotic lipoxygenases contains a PLAT domain (see <PDOC50095>) that may be involved in membrane-binding or substrate acquisition, while the iron-binding catalytic domain forms the C-terminal part.

The 3D structure of the catalytic domain is mainly α-helical with an iron in the active site (see <PDB:1F8N>). The center of the domain consists of two long helices, which contain four of the iron-binding residues (at least three of which are histidines). A fifth residue that coordinates the non-heme catalytic iron is the carboxylate of the C-terminal isoleucine. The mammalian catalytic domain has a length of ~550-600 residues, which is shorter than in the plant lipoxygenases and forms a more compact structure as the additional 100-150 amino acids in plant enzymes form extra loops [3,6,7].

Some proteins known to contain a lipoxygenase iron-binding catalytic domain:

• Plant lipoxygenases (EC 1.13.11.12). Plants express a variety of cytosolic isozymes as well as what seems [8] to be a chloroplast isozyme.
• Mammalian arachidonate 5-lipoxygenase (EC 1.13.11.34).
• Mammalian arachidonate 12-lipoxygenase (EC 1.13.11.31).
• Mammalian erythroid cell-specific 15-lipoxygenase (EC 1.13.11.33).
• Coral (Plexaura homomalla) allene oxide synthase-lipoxygenase protein, a bifunctional enzyme including both a peroxidase and arachidonate 8-lipoxygenase (EC 1.13.11.40).
• Pseudomonas aeruginosa oleic acid lipoxygenase and arachidonate 15-lipoxygenase (EC 1.13.11.33).

Six histidines are strongly conserved in lipoxygenase sequences, five of them are found clustered in a stretch of 40 amino acids. This region contains two of the three iron-ligands; the other histidines have been shown [9] to be important for the activity of lipoxygenases. As signatures for this family of enzymes we have selected two patterns in the region of the histidine cluster. The first pattern contains the first three conserved histidines and the second pattern includes the fourth and the fifth. We also developed a profile that covers the entire lipoxygenase iron-binding catalytic domain.