An unusual activity of mycobacterial MutT1 Nudix hydrolase domain as a protein phosphatase regulates nucleoside diphosphate kinase function
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Abstract
MutT proteins are Nudix hydrolases characterized by the presence of a Nudix box, GX5EX7REUXEEXGU, where U is a bulky hydrophobic residue and X is any residue. Major MutT proteins hydrolyze 8-oxo-(d)GTP (8-oxo-GTP or 8-oxo-dGTP) to the corresponding 8-oxo-(d)GMP, preventing their incorporation into nucleic acids. Mycobacterial MutT1 comprises an N-terminal domain (NTD) harboring the Nudix box motif, and a C-terminal domain (CTD) harboring the RHG histidine phosphatase motif. Interestingly, unlike other MutTs, the MutT1 hydrolyses the mutagenic 8-oxo-(d)GTP to the corresponding 8-oxo-(d)GDP. Nucleoside diphosphate kinase (NDK), a conserved protein, carries out reversible conversion of (d)NDPs to (d)NTPs through phospho-NDK (NDK- Pi ) intermediate. Recently, we showed that NDK- Pi converts 8-oxo-dGDP to 8-oxo-dGTP and escalates A to C mutations in a MutT-deficient Escherichia coli . We now show that both Mycobacterium tuberculosis MutT1 and Mycobacterium smegmatis MutT1, through their NTD (Nudix hydrolase motifs) function as protein phosphatase to regulate the levels of NDK- Pi and prevent it from catalyzing conversion of (d)NDPs to (d)NTPs (including conversion of 8-oxo-dGDP to 8-oxo-dGTP). To corroborate this function, we show that Msm MutT1 decreases A to C mutations in E. coli under the conditions of Eco NDK overexpression. IMPORTANCE: MutT proteins, having a Nudix box domain, hydrolyze the mutagenic 8-oxo-dGTP to 8-oxo-dGMP. However, mycobacterial MutT (MutT1) comprises an N-terminal domain (NTD) harboring a Nudix box, and a C-terminal domain (CTD) harboring an RHG histidine phosphatase. Unlike other MutTs, mycobacterial MutT1 hydrolyses 8-oxo-dGTP to 8-oxo-dGDP. Nucleoside diphosphate kinase (NDK), a conserved protein, converts 8-oxo-dGDP to 8-oxo-dGTP through phospho-NDK (NDK- Pi ) intermediate and escalates A to C mutations. Here, we show that the mycobacterial MutT1 is unprecedented in that its NTD (Nudix box), functions as protein phosphatase to regulate NDK- Pi levels and prevents it from converting dNDPs to dNTPs (including 8-oxo-dGDP to 8-oxo-dGTP conversion). In addition, mycobacterial MutT1 decreases A to C mutations in Escherichia coli under the conditions of NDK overexpression.
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- Authors
- Emam, E. A. F., Roy, K., Singh, D. P., Saini, D. K., & Varshney, U.
- Affiliations
- Indian Institute of Science Bangalore (IN)
- Jawaharlal Nehru Centre for Advanced Scientific Research (IN)
- Corresponding author
- Varshney, Umesh
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2025-01-31
- Volume
- 207
- Issue
- 1
- Pages
- e0031424-e0031424
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- PMC
- PMC11784022
- OpenAlex
- W4405279568
- Cited by
- 5
- References
- 53
- Citations by year
- 2026: 2 · 2025: 3
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Bacteriology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department of Biotechnology, Ministry of Science and Technology, India (BT/PR50905/MED/29/1655/2023)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Nudix hydrolase, protein phosphatase, nucleoside diphosphate kinase, Mycobacterium tuberculosis, Mycobacterium smegmatis
- MeSH terms
- Protein Domains, Nudix Hydrolases, Bacterial Proteins, Deoxyguanine Nucleotides, Escherichia coli, Mycobacterium tuberculosis, Nucleoside-Diphosphate Kinase, Phosphoprotein Phosphatases, Pyrophosphatases, Gene Expression Regulation, Bacterial, Mycobacterium smegmatis
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