An updated view on the structure and function of PYRIN domains

Abstract

The PYRIN domain (PYD) is a protein-protein interaction domain, which belongs to the death domain fold (DDF) superfamily. It is best known for its signaling function in innate immune responses and particularly in the assembly of inflammasomes, which are large protein complexes that allow the induced proximity-mediated activation of caspase-1 and subsequently the release of pro-inflammatory cytokines. The molecular mechanism of inflammasome assembly was only recently elucidated and specifically requires PYD oligomerization. Here we discuss the recent advances in our understanding of PYD signaling and its regulation by PYD-only proteins.

Figure 1

Domain architecture of human and mouse PYD-containing (a) NLRPs, (b) ALRs, and (c) regulatory proteins. The number of the amino acid residues of the longest isoform is indicated.

Figure 2

The residues in the ASC-PYD comprising the hydrophobic core, which are necessary for the overall PYD fold, are indicated. A similar hydrophobic core is present in all PYDs.

Figure 3

PYDs with known NMR or crystal structure are shown as Ribbon diagram and Electrostatic surface representation. The left panel of each PYD (including ribbon and surface) are shown in the same orientation. The right panels of the each PYD is rotated by 180° along the vertical axis. α helices in the Ribbon diagram are shaded in orange (α1), green (α2), yellow (α3), purple (α4), cyan (α5), and magenta (α6). The electrostatic charge surfaces are displayed on a scale of -4 kT/e (red) to 4 kT/e (blue). Notable are the lack of α3 in the NLRP1-PYD, the strongly negatively charged surface in NLRP7, the fused α5–α6 helix in the NLRP14-PYD and the extended α6 helix in the AIM2-PYD. NLRP1-PYD (PDB: 1PN5) [42], NLRP3-PYD (PDB: 3QF2) [18], NLRP4-PYD (PDB: 4EWI) [46], NLRP7-PYD (PDB: 2KM6) [45], NLRP10-PYD (PDB: 2M5V), NLRP12-PYD (PDB: 2L6A) [47], NLRP14-PYD (PDB: 4N1J) [49], AIM2-PYD (PDB: 3VD8) [50], ASC-PYD (PDB: 1UCP) [43], POP1-PYD (PDB: 2HM2) [44, 98, 99].

Figure 4

CLUSTAL-W alignment of (a) human and (b) mouse PYDs, showing acidic residues (red), basic residues (blue) and hydrophobic residues (grey). α-helices determined by NMR or crystal structure are boxed in black and the Hin-200 specific motifs are boxed in yellow and marked by a yellow line on top, as identified earlier [50].

Figure 5

The three types of ASC PYD interactions (type I, type II, and type III) [8, 59, 78, 107]. Negative charge is marked in red, positive charge is marked in blue, and neutral residues are marked in pink. The ASC-PYD polymer is comprised of three-start helical strands with C3 symmetry, resulting from type 1 interaction in each of the strands and type 2 and type 3 interactions between the strands [59, 78]. A model of the polymer is indicated, showing the interactions in the start helices on the bottom left [59].

Figure 6

Model of inflammasome assembly. NLRP3 or AIM2 (not shown) nucleate ASC-PYD polymerization. (a) The polymeric assembly of ASC and caspase-1 and (b) a cross section of the polymer has been modified from Lu and colleagues [59]. (c) An alternative model, observed in macrophages after Salmonella infection, modified from Man and colleagues [93]. In this model, the sensors are composed of a complex of NLRP3 and NLRC4 (not shown).

Figure 7

Phylogenetic tree analysis of (a) human and (b) mouse PYDs, showing POPs for each of the major PYD cluster in humans and lack of these proteins in mice. PYDs linked to inflammasome activation are highlighted in green and the POPs in red. Method: Neighbor Joining; Best Tree; tie breaking = Systematic Distance: Uncorrected (“p”), Gaps distributed proportionally.

Figure 8

Type I interaction between two ASC-PYDs, ASC-PYD - POP1 and ASC-PYD - NLRP3-PYD, showing the overlapping interaction motif as identified by mutagenesis [78, 97].

Figure 9

Proposed mechanism for the function of POPs, which either may bind to (a) the ASC-PYD, as demonstrated for POP1 and POP2 [21, 100, 102], or to (b) the PYD of upstream sensors, as shown for POP2 and POP3 [100, 103].