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Cited by 0Enzyme Structure and FunctionProtein Structure and DynamicsMicrobial metabolism and enzyme function

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Bifunctional architecture enables substrate catalysis and channeling in Paracoccus TMAO demethylase

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Thach, Trung, Dhanabalan, KanagaVijayan, Maurya, Shiwangi, Han-Hallett, Yu, Quan, Senwei, Allison, Jane, Ramanathan, Gurunath, Subramanian, Ramaswamy·2026·eLife
DOI 10.7554/elife.109964

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Abstract

Substrate channeling enhances efficiency and prevents toxicity by directing unstable intermediates between active sites. Trimethylamine N-oxide demethylase (TDM) degrades trimethylamine N-oxide (TMAO) to dimethylamine and formaldehyde (HCHO), but the fate of HCHO has remained unclear. We report cryo-EM structures of TDM in apo, substrate-, and product-bound states that reveal a previously unknown channeling pathway. Combined structural, biochemical, and target molecular dynamics analyses show that HCHO is generated in a catalytic core and guided through a tunnel to a remote tetrahydrofolate (THF)-binding site, where it forms methylene-THF. Thus, TDM emerges as a bifunctional enzyme that unites TMAO demethylation with one-carbon transfer, providing a mechanistic explanation for its role in metabolic efficiency and detoxification.

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Metadata

Authors
Thach, T., Dhanabalan, K., Maurya, S., Han-Hallett, Y., Quan, S., Allison, J., Ramanathan, G., & Subramanian, R.
Affiliations
  • Purdue University West Lafayette (US)
  • Indian Institute of Technology Kanpur (IN)
  • Bindley Bioscience Center, Purdue University
  • University of Auckland (NZ)
  • Department of Biological Sciences, Purdue University
Corresponding author
  • Thach, Trung
  • Ramanathan, Gurunath
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2026-09-28
Volume
15
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.109964
OpenAlex
W7130389363
Cited by
0
References
1
Type
posted content
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
Keywords
substrate channeling, bifunctional enzyme, enzyme mechanism, formaldehyde toxicity, Paracoccus
MeSH terms
Catalysis, Dimethylamines, Formaldehyde, Methylamines, Oxidoreductases, N-Demethylating, Paracoccus, Protein Conformation, Substrate Specificity, Tetrahydrofolates, Catalytic Domain, Cryoelectron Microscopy, Molecular Dynamics Simulation

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