The Structure, Activity, and Function of the SETD3 Protein Histidine Methyltransferase

Abstract

SETD3 has been recently identified as a long sought, actin specific histidine methyltransferase that catalyzes the Nτ-methylation reaction of histidine 73 (H73) residue in human actin or its equivalent in other metazoans. Its homologs are widespread among multicellular eukaryotes and expressed in most mammalian tissues. SETD3 consists of a catalytic SET domain responsible for transferring the methyl group from S-adenosyl-L-methionine (AdoMet) to a protein substrate and a RuBisCO LSMT domain that recognizes and binds the methyl-accepting protein(s). The enzyme was initially identified as a methyltransferase that catalyzes the modification of histone H3 at K4 and K36 residues, but later studies revealed that the only bona fide substrate of SETD3 is H73, in the actin protein. The methylation of actin at H73 contributes to maintaining cytoskeleton integrity, which remains the only well characterized biological effect of SETD3. However, the discovery of numerous novel methyltransferase interactors suggests that SETD3 may regulate various biological processes, including cell cycle and apoptosis, carcinogenesis, response to hypoxic conditions, and enterovirus pathogenesis. This review summarizes the current advances in research on the SETD3 protein, its biological importance, and role in various diseases.

Keywords: SETD3; actin; cytoskeleton; enteroviruses; oncogenesis; polymerization; posttranslational modifications; protein histidine methylation.

Figure 1

Reactions catalyzed by protein histidine N-methyltransferases. At pH ≈ 7, two neutral tautomers of histidine residues may exist in proteins: the N1-protonated π-tautomer and the N3-protonated τ-tautomer. Data show that different protein histidine methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to specific nitrogen of the imidazole ring. HPM1, SETD3, METTL9, and METTL18 are the only enzymes characterized with this activity so far. AdoHcy—S-adenosyl-L-homocysteine.

Figure 2

Structure of human SETD3. (A) Domain composition of SETD3. Waved lines correspond to the disordered regions at the N-terminal and C-terminal of the protein. Red bars indicate the localization of amino acid residues at which AdoMet binds to SETD3. Data were retrieved from the NCBI Protein database (accession number: XP_011535533.2, accessed on 30 July 2021). (B) Conformation of human SETD3 (residues 2–502) in complex with the peptide substrate derived from β-actin (residues 66–88) and close up view of the SETD3 substrate binding cleft with molecular surfaces. The image was created in UCSF Chimera 1.15 software utilizing the coordinates deposited in Protein Data Bank file 6ICV [36]. The color scheme of domains is common in Figure 2 and Figure 3.

Figure 3

Amino acid residues of SETD3 that are important for proper recognition and alignment of H73 of β-actin to AdoMet prior to methylation. The image was created in UCSF Chimera 1.15 software utilizing the coordinates deposited in Protein Data Bank file 6ICV [36]. The color scheme of domains is common in Figure 2 and Figure 3.

Figure 4

Structural alignment of SETD3 amino acid residues interacting with H73 of β-actin and conserved residues of SETD4. The image was created in UCSF Chimera 1.15 software utilizing the coordinates deposited in Protein Data Bank file 6ICV and the SETD4 structure predicted by AlphaFold [41] using UniProt Q9NVD3 record as an input. Structural alignment was calculated using the MatchMaker tool in UCSF Chimera 1.15 software [36].

Figure 5

Structures of human β-actin. Ribbon representations of the structures of the actin monomer are shown in different projections. The actin molecule consists of small and large domains (red and blue, respectively), and each one is divided further into two subdomains: 1, 2, and 3, 4, respectively. ATP (or ADP) binds to the cleft between subdomains 2 and 4. The methyl-accepting H73 is located in a sensor loop spanning P70 to N78 (green). This residue is exposed to the surface of the actin monomer and seems to be easily accessible for SETD3. The model was prepared using UCSF Chimera [36] from the Protein Data Bank structures of β-actin (2BTF).

Figure 6

Plausible mechanisms of actin histidine Nτ-methylation by SETD3. The enzyme catalyzes the methylation of Nτ nitrogen atom of H73 residue in actin. The methyl group of AdoMet can be transferred only to the deprotonated nitrogen atom. Since each of the two nitrogen atoms of the imidazole ring can hypothetically be protonated, the side chain of N256 residue of SETD3 stabilizes the Nπ nitrogen atom of H73 in the protonated form [32]. Consequently, it enhances the nucleophilicity of the lone pair of electrons present at the deprotonated Nτ nitrogen that may then attack the methyl group of AdoMet.

Figure 7

SETD3 expression in human tissues. RNA data were obtained from the Human Protein Atlas (HPA; https://www.proteinatlas.org, accessed on 29 July 2021) and show consensus normalized expression levels, determined by combining the data from three transcriptomic datasets (HPA, Genotype-Tissue Expression, and FANTOM5) [53]. Color coding is based on tissue groups, each consisting of tissues with common functional features.

Figure 8

Scheme of nucleotide exchange under steady state during actin polymerization. During the steady state phase of polymerization, ADP–actin complexes dissociate from the pointed end (-) of the filamentous actin. This is followed by nucleotide exchange (from ADP to ATP) and, consequently, ATP–actin associates mainly at the barbed end (+). ATP hydrolysis allows the translocation of subunits between the ends of the filament [45]. SETD3 is found to promote actin polymerization through H73 methylation [18].