Computational analyses of the effect of novel amino acid clusters of human transglutaminase 2 on its structure and function

Abstract

Transglutaminase 2 (TGM2) is a unique protein of a nine member family with several enzymatic and non-enzymatic activities and interacting partners. Its physiological and pathological roles, however, are not fully understood. Comparative genomic and computational analysis reported here have revealed phylogenetic changes of TGM2 resulting in novel amino acid clusters in humans and other primates, which may impact secondary structure and increase protein stability. These clusters are located in intrinsically disordered regions and via short linear motifs influence interactions with TGM2 partners directly, or through post-translation modification (phosphorylation and N-glycosylation sites). Our data shed new light on the structural background and evolution of TGM2 multi-functionality and points to so far unrevealed biological roles of the enzyme.

Genomic variants reveal differential evolutionary constraints on human transglutaminases and point towards unrecognized significance of transglutaminase 2

“…Lane 1: sequence of human TGM2, Lane 2: damaging nsSNVs in human TGM2. Functional regions of human TGM2: Intrinsically disordered regions (dark red) [ 4 ], amino acid clusters in light blue [ 30 ], fibronectin binding sites (FN) (green) K30, R116, and H134 [ 31 ], GDP binding residues (orange) S171, K173, R476, R478, V479, R580, Y583 [ 32 ], catalytic residues (pink); non-canonical Ca 2+ -binding sites: S4: 149–159, S1: 228–236, S3A: 305–311, S3B: 326–333, S2A: 395–401, S5: 432–440, and S2B: 445–455 (underlined and bolded) [ 33 ]. Domains of human TGM2 are presented vertically: β sandwich (1–139), catalytic core (147–460), β-barrel 1 (472–583), and β-barrel 2 (584–687).…”

“…Damaging nsSNVs are not present at active site residues (W241, C277, H335, and D358) and at recently described novel amino acid clusters emerged in humans [ 30 ]. We have previously identified additional residues around the active site, which are crucial for transamidase (W278) or isopeptidase (W332) activity [ 29 ] and there are no damaging nsSNV at these sites either.…”

“…A PolyPhen damaging variant with decreased activity is p.Val542Phe located within the MOD CK1 phosphorylation site and MOD PLK site phosphorylated by polo like kinases. Another potentially damaging variant p.Pro612Thr with less transamidase, isopeptidase and GTP binding is near to an IDR (597–602) and a novel amino acid cluster PVA (613–615) [ 30 ]. The homozygous variant p.Asp671Asn is located in the C-terminal class 3 PDZ-binding motif.…”

Spotlight on the transglutaminase 2 gene: a focus on genomic and transcriptional aspects

“…The white rhombus represents mutation N333S in a subject with MODY [43,45]. Triangles and bars represent SNPs detected in functional regions: cyan, SNPs in FN-binding site; violet, SNPs in amino acids probably significant for human TGM2 activities as described by Thangaraju et al [37]; black, SNPs in epitopes interacting with coeliac antibodies; green, SNPs in Bcl-2 protein family motif; grey, SNPs in nuclear location signals; yellow, SNP in amino acid in non-proline cis peptide bonds; orange, SNPs in putative Ca 2+ -binding sites; red, SNPs in GDP-binding and GTPase sites; brilliant green, SNPs in peptide regions involved in recognition and activation by the α1 B -adrenergic receptor; brown, SNPs in domain for PLCδ1 recognition. (B) Effects of SNP on the variant phenotype from the web site (http://snpeffect.switchlab.org/menu).…”

“…Supplementary Table S1 also lists the SNPs involved in alterations at 'amino acid clusters' of TG2 that were recently investigated by Thangaraju et al [37]. These authors focused attention on short sequences of 3-4 amino acids differing in murine and human TG2, which could be engaged in functional activity or stability of the protein, in the interaction with other proteins and in target sites for post-translational modifications.…”