Nature’s Molecular Scissors: How Bacteria Use Nitrogenase Machinery to Cleave Tough Carbon-Sulfur Bonds

Revolutionary Enzyme Discovery Challenges Nitrogenase Paradigm

In a groundbreaking study published in Nature Catalysis, researchers have uncovered how bacteria deploy nitrogenase-like metalloclusters for an entirely different purpose: cleaving stubborn carbon-sulfur bonds in methylthio-alkanes. The methylthio-alkane reductase system, encoded by marHDK genes, represents a fascinating example of nature repurposing complex molecular machinery for new chemical transformations.

Structural Architecture Reveals Nitrogenase Similarities

Scientists heterologously produced the methylthio-alkane reductase components MarH, MarD, and MarK from R. rubrum in engineered Rhodobacter capsulatus strains. Through sophisticated purification and mass photometry techniques, they determined the enzyme complex consists of a MarH homodimer (69 kDa) and a Mar(DK) heterotetramer (227 kDa) – mirroring the stoichiometry of conventional Mo-nitrogenase components., as detailed analysis, according to expert analysis

The purified enzymes demonstrated remarkable activity, reducing various volatile organic sulfur compounds including MT-EtOH, EMS, and DMS at rates between 2.3-7.9 nmol CH × mg Mar(DK) × min. Crucially, this activity proved ATP-dependent and required both reductase and catalytic components along with sodium dithionite as an electron donor., according to industry developments

Cryo-EM Breakthrough Reveals Metallocluster Secrets

Determining the molecular structure presented significant challenges due to preferential orientation bias and MarD’s susceptibility to denaturation. Researchers ingeniously overcame these obstacles by forming a complex using MgADP-AlF₄^– to stabilize the catalytic component., according to market insights

Through sophisticated classification strategies and focused refinement, the team achieved a 2.75 Å resolution structure revealing the enzyme’s remarkable metallocluster architecture. The structure shows a conventional reductase component (MarH) containing a [4Fe-4S] cluster, which transfers electrons to a P-cluster located approximately 15.0 Å away., according to industry reports

Unexpected Metallocluster Composition

The most exciting discovery emerged at the active site, where researchers identified a [Fe₈C₉S] cluster – identical to the FeMoco precursor from nitrogenase systems. ICP-OES analysis confirmed 32.6 ± 5.3 iron atoms per catalytic component, consistent with two P-clusters and two [Fe₈C₉S] clusters per Mar(DK) heterotetramer.

Notably absent were both molybdenum and vanadium, and HPLC-MS analysis failed to detect (R)-homocitrate – a key component of conventional nitrogenase cofactors. This makes methylthio-alkane reductase the only known Nfl enzyme to harbor both the complex P-cluster and [Fe₈C₉S] cluster.

Unique Coordination Environment Enables Specialized Function

The [Fe₈C₉S] cluster anchors to the protein scaffold through only two amino acid residues: Cys270 coordinating Fe1 and His429 coordinating Fe8. This contrasts sharply with nitrogenase systems, where additional coordination occurs through (R)-homocitrate.

The bond distance between His429 and Fe8 measures just 1.9 Å – significantly shorter than comparable bonds in Mo-nitrogenase (3.1 Å) or Fe-nitrogenase (2.7 Å). This unique coordination geometry necessitates the presence of an interstitial carbide for structural stability.

Specialized Active Site for Carbon-Sulfur Bond Cleavage

The active site environment differs substantially from nitrogenases. Where nitrogenases feature Val70, Gln191, and His195 surrounding the S2B site, methylthio-alkane reductase presents Cys73, Gln74, Trp195, and Phe199. Due to a 48° rotation of the S2B site relative to FeMoco, only Trp195 positions close enough to form hydrogen bonds.

This distinctive arrangement of Trp195, His194, and His375 around the S2B site at distances of 3.9-4.7 Å suggests specialized mechanisms for substrate recognition, binding, and proton transfer during carbon-sulfur bond cleavage.

Implications for Biotechnology and Environmental Science

This discovery opens new avenues for:

• Environmental remediation – developing biological solutions for sulfur compound contamination
• Biocatalysis – engineering enzymes for industrial desulfurization processes
• Evolutionary biology – understanding how nature repurposes complex molecular machinery
• Renewable energy – potential applications in biofuel processing and sulfur removal

The methylthio-alkane reductase system demonstrates nature’s remarkable ability to adapt sophisticated metalloenzyme architecture for specialized chemical tasks, providing both fundamental insights into enzyme evolution and practical applications for challenging chemical transformations.

References

• http://www.rcsb.org/structure/7UTA
• http://www.rcsb.org/structure/8OIE

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