Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation.
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| Format: | Artículo científico |
| Sprache: | en |
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International journal of biological macromolecules
2026
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| author | Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua |
| author_facet | Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua |
| collection | PubMed - marine biology |
| contents | Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation. Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua Pyrophosphatases Substrate Specificity Methanosarcina Molecular Dynamics Simulation Phylogeny Catalytic Domain Evolution, Molecular Protein Domains Amino Acid Sequence Mutagenesis, Site-Directed Models, Molecular Archaeal Proteins Structure-Activity Relationship Protein Binding Archaeal dUTPases remain poorly understood despite their critical role in nucleotide metabolism. Here, we report the crystal structures of a trimeric dUTPase from Methanosarcina mazei in apo and dUTP-bound forms at 1.45 Å and 1.53 Å resolution, respectively. Unlike canonical dUTPases that utilize conserved motif V for active-site formation, this enzyme employs a unique structural insertion (subdomain I) to coordinate the γ-phosphate of dUTP and stabilize the trimer interface. Site-directed mutagenesis (N55A and R58A) confirmed the catalytic relevance of subdomain I. Molecular dynamics simulations revealed ligand-induced stabilization of the otherwise flexible C-terminal region. Comparative structural and phylogenetic analyses placed this archaeal enzyme within the Type II dUTPase clade but highlighted its distinctive mechanism of substrate recognition. These findings uncover an alternative structural strategy for maintaining enzymatic activity in the absence of motif V, expanding our understanding of dUTPase diversity and offering a potential framework for engineering robust nucleotide-processing enzymes. |
| format | Artículo científico |
| id | pubmed_41308777 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | International journal of biological macromolecules |
| record_format | pubmed |
| spellingShingle | Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation. Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua Pyrophosphatases Substrate Specificity Methanosarcina Molecular Dynamics Simulation Phylogeny Catalytic Domain Evolution, Molecular Protein Domains Amino Acid Sequence Mutagenesis, Site-Directed Models, Molecular Archaeal Proteins Structure-Activity Relationship Protein Binding Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation. Chen, Sheng-Chia Chou, Chun-Chi Chen, Wen-Ming Sheu, Shih-Yi Huang, Liang-Wei Huang, Cheng-Hung Chang, San-Chi Kuo, Chia-Hung Hsu, Chun-Hua Pyrophosphatases Substrate Specificity Methanosarcina Molecular Dynamics Simulation Phylogeny Catalytic Domain Evolution, Molecular Protein Domains Amino Acid Sequence Mutagenesis, Site-Directed Models, Molecular Archaeal Proteins Structure-Activity Relationship Protein Binding Archaeal dUTPases remain poorly understood despite their critical role in nucleotide metabolism. Here, we report the crystal structures of a trimeric dUTPase from Methanosarcina mazei in apo and dUTP-bound forms at 1.45 Å and 1.53 Å resolution, respectively. Unlike canonical dUTPases that utilize conserved motif V for active-site formation, this enzyme employs a unique structural insertion (subdomain I) to coordinate the γ-phosphate of dUTP and stabilize the trimer interface. Site-directed mutagenesis (N55A and R58A) confirmed the catalytic relevance of subdomain I. Molecular dynamics simulations revealed ligand-induced stabilization of the otherwise flexible C-terminal region. Comparative structural and phylogenetic analyses placed this archaeal enzyme within the Type II dUTPase clade but highlighted its distinctive mechanism of substrate recognition. These findings uncover an alternative structural strategy for maintaining enzymatic activity in the absence of motif V, expanding our understanding of dUTPase diversity and offering a potential framework for engineering robust nucleotide-processing enzymes. |
| title | Structural and functional insights into an archaeal dUTPase reveal a subdomain-mediated mechanism for substrate recognition and evolutionary adaptation. |
| topic | Pyrophosphatases Substrate Specificity Methanosarcina Molecular Dynamics Simulation Phylogeny Catalytic Domain Evolution, Molecular Protein Domains Amino Acid Sequence Mutagenesis, Site-Directed Models, Molecular Archaeal Proteins Structure-Activity Relationship Protein Binding |
| url | https://pubmed.ncbi.nlm.nih.gov/41308777/ |