PROSITE documentation PDOC00224

Tumor necrosis factor (TNF) homology domain (THD) signature and profile

The tumor necrosis factor (TNF) superfamily, composed of 19 ligands and 29 receptors, plays highly diversified roles in the body. All members of the TNF superfamily, without exception, exhibit pro-inflammatory activity, in part through activation of the transcription factor NF-kappaB. Ligands and receptors of the TNF superfamilies are examples of signal transducers whose integrated actions impinge principally on the development, homeostasis and adaptative responses of the immune system. The TNF ligand family comprises 18 genes encoding 19 type II (i.e. intracellular N terminus and extracellular C terminus) transmembrane proteins. Although most ligands are synthesized as membrane-bound proteins, soluble forms can be generated by limited proteolysis. That the 19 members of the TNF ligand family interact with 29 distinct receptors implies that at least some of the ligands must interact with more than one receptor. Despite their varied and pleiotropic actions, members of the TNF ligand and receptor (TNFR) families have remarkably similar structures, and their mode of interaction is conserved. TNF ligands share a common structural motif, the TNF homology domain (THD), which binds to cysteine-rich domains (CRDs) of TNF receptors [1,2].

The THD is a 150 amino acid long sequence containing a conserved framework of aromatic and hydrophobic residues. The THDs are β-sandwich structures containing two stacked β-pleated sheets each formed by five anti-parallel β strands that adopt a classical 'jelly-roll' topology (see <PDB:3QD6>. The active form of TNFs appears to be a trimeric molecule. The inner sheet (strands A, A', H, C and F) is involved in trimer contacts, and the outer sheet (strands B, B', D, E and G) is exposed at the surface. The extensive trimerization interface between the subunits is formed mostly by hydrophobic residues. Trimeric THDs resemble bell-shaped, truncated pyramids with variable loops protruding out of a compact core of conserved anti-parallel β strands. The THD and globular C1q (see <PDOC00857>) domains have a closely related tertiary structure and trimeric organization, suggestive of an evolutionary link between the TNF and C1q families [2,3,4].

The TNF ligand family can roughly be divided into three groups (the conventional, the EF-disulfide-containing, and the divergent) based on sequence and structural features [5]:

The conventional ligands are all expected to bind receptors in a similar manner in part because they all have, in the DE loop, a conserved hydrophobic residue (generally a tyrosine) which has been shown to be energetically important for receptor binding in several of the family members. The conventional TNF ligand members include:

• Tumor Necrosis Factor (TNF) (also known as cachectin or TNF-α) [6,7] is a cytokine which has a wide variety of functions. It can cause cytolysis of certain tumor cell lines; it is involved in the induction of cachexia; it is a potent pyrogen, causing fever by direct action or by stimulation of interleukin-1 secretion; finally, it can stimulate cell proliferation and induce cell differentiation under certain conditions.
• Lymphotoxin-α (LT-α), or TNF-β, is produced by lymphocytes and is cytotoxic for a wide range of tumor cells in vitro and in vivo [3,8].
• Lymphotoxin-β (LT-β) may play a specific role in immune response regulation. It provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface.
• TNF-related apoptosis inducing ligand (TRAIL) [9], a cytokine that induces apoptosis [9].
• Vascular endothelial cell-growth inhibitor (VEGI) mediates activation of NF-kappa-B and promotes activation of caspases and apoptosis.
• LT-related inducible ligand that competes for glycoprotein D binding to herpes virus entry mediator on T cells (LIGHT) functions in both a soluble and cell surface-bound manner to interact with two primary functional receptors: herpes virus entry mediator (HVEM) and lymphotoxin-β receptor (LTβR).
• FASL, a cytokine involved in cell death [10].
• Receptor activator of NF-kappaB ligand (RANKL), an osteoclast differentiation and activation factor.
• T cell antigen gp39 (also called CD40L or CD154), a cytokine which seems to be important in B-cell development and activation [4].

Members of the second TNF ligand group, the EF-disulfide group, all possess a disulfide connecting the E and F strands and are characterized by shorter CD and EF loops, resulting in a more globular shape. This group consists of:

• A proliferation-inducing ligand (APRIL) plays a role in the regulation of tumor cell growth and may be involved in monocyte/macrophage-mediated immunological processes.
• B-cell activating factor (BAFF) is a B-cell survival factor.
• TNF-related weak inducer of apoptosis (TWEAK) is a weak inducer of apoptosis in some cell types and mediates NF-kappa-B activation.
• Ectodysplasin A (EDA)-A1 and EDA-A2 are splice variants with distinct receptor specificity. EDA-A1 binds EDAR, a member of the TNFR family involved in ectodermal development, while EDA-A2 binds to the related receptor, XEDAR [11].

The third, divergent, ligand group contains the remaining members of the TNF ligand family. These ligands all have sequences that are very divergent from each other and from either the conventional or EF-disulfide groups:

• CD27L, a cytokine which plays a role in T-cell activation. It induces the proliferation of costimulated T cells and enhances the generation of cytolytic T cells.
• CD30L, a cytokine which induces proliferation of T cells.
• Glucocorticoid-induced TNF-related ligand (GITRL)
• 4-1BBL, a inducible T cell surface molecule that contributes to T-cell stimulation.
• OX40L, a cytokine that co-stimulates T cell proliferation and cytokine production [5,12].

As a signature for this family of proteins, we have selected the most conserved region. This region is located in a β-strand in the central section of these proteins. We also developed a profile that covers the entire THD domain.