Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2

Abstract

Sirtuins were originally shown to regulate a wide array of biological processes such as transcription, genomic stability, and metabolism by catalyzing the NAD+-dependent deacetylation of lysine residues. Recent proteomic studies have revealed a much wider array of lysine acyl modifications in vivo than was previously known, which has prompted a reevaluation of sirtuin substrate specificity. Several sirtuins have now been shown to preferentially remove propionyl, succinyl, and long-chain fatty acyl groups from lysines, which has changed our understanding of sirtuin biology. In light of these developments, we revisited the acyl specificity of several well-studied archaeal and bacterial sirtuins. We find that the Archaeoglobus fulgidus sirtuins, Sir2Af1 and Sir2Af2, preferentially remove succinyl and myristoyl groups, respectively. Crystal structures of Sir2Af1 bound to a succinylated peptide and Sir2Af2 bound to a myristoylated peptide show how the active site of each enzyme accommodates a noncanonical acyl chain. As compared to its structure in complex with an acetylated peptide, Sir2Af2 undergoes a conformational change that expands the active site to accommodate the myristoyl group. These findings point to both structural and biochemical plasticity in sirtuin active sites and provide further evidence that sirtuins from all three domains of life catalyze noncanonical deacylation.PDB Code(s): 4TWI; 4TWJ

Human SIRT3 tripeptidic inhibitors containing Nε-thioacetyl-lysine

“…[1][2][3] While the typical acyl group is acetyl, those bulkier than acetyl have also been recently identified, such as succinyl, glutaryl, and myristoyl. Lysine N e -acylation can be accomplished enzymatically (e.g., catalyzed by protein N e -acetyltransferases) or non-enzymatically (e.g., realized in mitochondrial matrix 4 due to the high concentration (mM range) for certain acyl-CoAs and the slightly basic pH ($8)) ( Fig.…”

“…3,[5][6][7][8][9] While the former family members achieve deacylation via a Zn 2+ -assisted hydrolysis of the side chain amide bond of N e -acyl-lysine, sirtuins employ a unique b-NAD + -dependent strategy to achieve deacylation in that N e -acyl-lysine is condensed with b-NAD + with the formation of three products in the same reaction, that is, nicotinamide, deacylated product, and 2 0 -O-AADPR (Fig. 1).…”

“…The chemical structures of the four further derivatives(19)(20)(21)(22) designed from a structure-activity-relationship analysis of the initial 16 derivatives(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18).…”

“…[3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] Figs. 3 and 4) were prepared by the Fmoc-chemistry based manual solid phase peptide synthesis (SPPS), as outlined in Scheme 1.…”

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

“…Specifically, the strictly conserved phenylalanine 190 and proline 221 (of E. coli Sir2/cobB protein) are present, in contrary the bacterial conserved tyrosine 220 is replaced by the polarly neutral amino acid Asparagine. This is a somewhat usual replacement also present in at least Archaea Archaeoglobus fulgidus’ Sir2Af1 (Ringel et al, 2014) and the human SIRT2 protein (Feldman et al, 2015), with the polarly neutral glutamine replacing tyrosine and remaining functional. Finally, valine 219 of E. coli is replaced with isoleucine, both being non-polar aliphatic amino acids.…”