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The gene symbol NIT1 in Saccharomyces cerevisiae (strain ATCC 204508 / S288c) corresponds to the systematic name YIL164C (UniProt accession P40447). The encoded protein is designated "Putative nitrilase-like protein Nit1" and belongs to the carbon-nitrogen hydrolase superfamily (branch 10 of the nitrilase superfamily). It should be noted that this yeast NIT1 is distinct from the plant nitrilase genes also called NIT1 (e.g., Arabidopsis NIT1 involved in auxin biosynthesis) and from the mammalian NIT1, though yeast Nit1 and mammalian Nit1 are true orthologs sharing conserved enzymatic function (peracchi2017nit1isa pages 1-1).
The landmark study by Peracchi et al. (2017) in Proceedings of the National Academy of Sciences definitively established that S. cerevisiae Nit1 (scNit1) is a metabolite repair enzyme that hydrolyzes deaminated glutathione (dGSH) (peracchi2017nit1isa pages 1-3, peracchi2017nit1isa pages 1-1). The enzyme catalyzes the hydrolysis of the amide bond in dGSH, converting the cyclic form of dGSH to α-ketoglutarate and cysteinylglycine (peracchi2017nit1isa pages 1-3). Based on this substrate specificity, the authors proposed renaming Nit1 and its orthologs as "dGSH amidases" (peracchi2017nit1isa pages 6-7).
Quantitative enzymatic characterization of recombinant scNit1 revealed striking substrate specificity. The enzyme exhibits a dGSH amidase specific activity of 8.71 ± 0.13 μmol·min⁻¹·mg⁻¹, compared to an ω-amidase specific activity (toward α-ketoglutaramate) of only 0.004 ± 0.000 μmol·min⁻¹·mg⁻¹, yielding a dGSH/α-KGM activity ratio of 2400 ± 35 (peracchi2017nit1isa pages 7-8). The enzyme shows negligible GSH amidase activity, negligible L-glutaminase activity, and minimal activity toward other physiologically present amides such as L-glutamine, γ-L-glutamyl-ε-L-lysine, N-acetyl-aspartylglutamate, and N-acetylglutamate (peracchi2017nit1isa pages 5-6, peracchi2017nit1isa pages 7-8). This demonstrates that dGSH is by far the best and most physiologically relevant substrate for Nit1.
The following table summarizes the enzymatic comparison between the two yeast nitrilase-family members:
| Property | scNit1 (S. cerevisiae NIT1/YIL164C) | scNit2 (S. cerevisiae NIT2) | Notes |
|---|---|---|---|
| Primary activity assignment | dGSH amidase | ω-amidase | Functional specialization is strongly divergent despite sequence similarity (peracchi2017nit1isa pages 1-1, peracchi2017nit1isa pages 1-3) |
| dGSH amidase specific activity (μmol·min⁻¹·mg⁻¹) | 8.71 ± 0.13 | < 0.001 | scNit1 is highly active toward deaminated glutathione; scNit2 is essentially inactive on this substrate (peracchi2017nit1isa pages 7-8) |
| ω-amidase specific activity toward α-KGM (μmol·min⁻¹·mg⁻¹) | 0.004 ± 0.000 | 3.59 ± 0.08 | scNit2 is the robust α-ketoglutaramate hydrolase; scNit1 shows only trace ω-amidase activity (peracchi2017nit1isa pages 7-8) |
| dGSH/α-KGM activity ratio | 2400 ± 35 | Near 0 | Quantifies extreme substrate preference of scNit1 for dGSH and scNit2 for α-KGM (peracchi2017nit1isa pages 7-8) |
| GSH amidase activity | Negligible | Not reported as substantial | scNit1 discriminates strongly against intact glutathione relative to deaminated glutathione (peracchi2017nit1isa pages 7-8) |
| L-glutaminase activity | Negligible | Not reported as substantial | Supports the conclusion that scNit1 is not a broad glutamine amidase (peracchi2017nit1isa pages 7-8, peracchi2017nit1isa pages 5-6) |
| Reaction catalyzed | Hydrolysis of deaminated glutathione (dGSH) to α-ketoglutarate + cysteinylglycine | Hydrolysis of α-ketoglutaramate to α-ketoglutarate + ammonia | Defines Nit1 as a metabolite-repair enzyme and Nit2 as a canonical ω-amidase (peracchi2017nit1isa pages 1-3, peracchi2017nit1isa pages 1-1) |
| Catalytic triad | Glu45-Lys127-Cys169 | Conserved Nit1/Nit2 family catalytic triad | Core carbon-nitrogen hydrolase active-site architecture (peracchi2017nit1isa pages 6-7) |
| Key substrate-recognition residues | Arg173, Phe195 | Distinct ω-amidase pocket features; Tyr87/Tyr254 signature described for Nit2-type enzymes | scNit1 structure indicates Arg173 and Phe195 help position and stabilize dGSH-like substrate at the active site (peracchi2017nit1isa pages 6-7) |
| Structural/functional interpretation | Highly specialized repair enzyme for damaged glutathione metabolite | Specialized enzyme in glutamine transaminase–ω-amidase pathway | Demonstrates how two branch-10 nitrilase-superfamily enzymes evolved different physiological substrates (peracchi2017nit1isa pages 6-7, peracchi2017nit1isa pages 1-1) |
Table: This table compares the enzymatic properties of the two Saccharomyces cerevisiae nitrilase-family proteins, highlighting that scNit1 is a deaminated-glutathione repair amidase whereas scNit2 is the canonical ω-amidase. It is useful for distinguishing substrate specificity, catalytic activity, and active-site features.
Despite sharing approximately 35% sequence identity with Nit2, Nit1 is functionally distinct (peracchi2017nit1isa pages 1-1). Nit2 (encoded by the yeast NIT2 gene) functions as an ω-amidase that hydrolyzes α-ketoglutaramate (α-KGM) to α-ketoglutarate and ammonia as part of the glutamine transaminase pathway (peracchi2017nit1isa pages 1-1, peracchi2017nit1isa pages 1-3). In contrast, scNit2 shows negligible dGSH amidase activity (<0.001 μmol·min⁻¹·mg⁻¹) but robust ω-amidase activity (3.59 ± 0.08 μmol·min⁻¹·mg⁻¹) (peracchi2017nit1isa pages 7-8). The two enzymes thus represent functional specialization within the same protein family.
The crystal structure of yeast scNit1 was solved and reveals the characteristic carbon-nitrogen hydrolase fold (peracchi2017nit1isa pages 6-7). The catalytic mechanism employs a catalytic triad composed of Glu45, Lys127, and Cys169, which is conserved across the Nit1/Nit2 family (peracchi2017nit1isa pages 6-7). Importantly, the crystal structure shows a GSH-like molecule bound at the active site, providing direct structural evidence for dGSH recognition (peracchi2017nit1isa pages 6-7).
Key residues involved in substrate recognition include Arg173, whose guanidino group interacts with the α-carboxylic group of the dGSH substrate, and Phe195, which makes π–π interactions with the keto group of the substrate (peracchi2017nit1isa pages 6-7). These interactions help position and stabilize dGSH for hydrolysis and contribute to distinguishing dGSH from other potential substrates such as native GSH.
A structural comparison with Nit2 reveals that the substrate specificity difference is related to the size of the subpocket for binding the amido group of α-KGM: this subpocket is much smaller in Nit2 due to the presence of two tyrosine residues (Tyr87 and Tyr254) that serve as a conserved signature for ω-amidases (peracchi2017nit1isa pages 6-7). The absence of these bulky residues in Nit1 accommodates the larger dGSH substrate.
Nit1 functions within the emerging paradigm of metabolite damage repair (also termed metabolite proofreading) (peracchi2017nit1isa pages 1-1, peracchi2017nit1isa pages 8-9, peracchi2017nit1isa pages 10-10). This concept recognizes that the normal catalytic promiscuity of abundant primary metabolic enzymes inevitably generates unwanted byproducts, which must be destroyed or reconverted into useful metabolites by dedicated repair enzymes (peracchi2017nit1isa pages 1-1). A significant proportion of the "catalytic dark matter" — enzymes of uncertain or unknown function encoded in sequenced genomes — may function in metabolite damage control (ellens2017confrontingthecatalytic pages 14-15). Indeed, Nit1 was considered among the "top 10" most attractive targets for functional assignment by Galperin and Koonin prior to the discovery of its dGSH amidase function (peracchi2017nit1isa pages 1-1).
Deaminated glutathione (dGSH) is generated as an inadvertent side product by multiple cytosolic and mitochondrial transaminases that use glutathione (GSH) as an amino group donor in slow, erroneous side-reactions (peracchi2017nit1isa pages 1-1, peracchi2017nit1isa pages 4-5, peracchi2017nit1isa pages 7-8). At least five mammalian transaminases (KYAT1, PSAT1, GOT1, KYAT3, and OAT) were demonstrated to catalyze GSH transamination at low rates (peracchi2017nit1isa pages 7-8). Although each individual reaction efficiency is small, the high intracellular concentration of GSH makes cumulative dGSH production significant over time (peracchi2017nit1isa pages 8-8). Evidence that aminooxyacetate (AOA), a general transaminase inhibitor, reduces dGSH accumulation in cultured cells confirms that transaminase activity is the primary source of dGSH formation in vivo (peracchi2017nit1isa pages 5-6). Additionally, at least one decarboxylase may also contribute to dGSH formation (peracchi2017nit1isa pages 8-8).
Critically, yeast strains lacking the NIT1 ortholog accumulate significantly elevated levels of dGSH, reaching an intracellular concentration of approximately 28 μM in knockout mutants compared to three- to seven-fold lower levels in wild-type controls (peracchi2017nit1isa pages 4-5). This accumulation demonstrates that Nit1 is the primary (or only) enzyme capable of metabolizing dGSH in yeast cells (peracchi2017nit1isa pages 4-5, peracchi2017nit1isa pages 1-1). The conservation of this phenotype across yeast, cultured mammalian cells, and mouse models confirms that Nit1-mediated dGSH hydrolysis is a conserved and physiologically important metabolic function (peracchi2017nit1isa pages 1-3, peracchi2017nit1isa pages 1-1).
In S. cerevisiae, Nit1 lacks a mitochondrial targeting sequence and is expected to function primarily in the cytoplasm. In the mammalian ortholog, two forms exist: a full-length form (mNit1) with a mitochondrial propeptide that localizes primarily to mitochondria (but also to the cytosol), and a shorter form (cNit1) lacking the mitochondrial targeting sequence that shows exclusively cytosolic localization (peracchi2017nit1isa pages 5-6). Mammalian Nit1 is thus found in both the cytosol and mitochondria — the "right places" where dGSH-forming transaminases are primarily located (peracchi2017nit1isa pages 8-8). In cultured mouse kidney cells, Nit1 is primarily distributed in the cytoplasm, with weaker nuclear and partial mitochondrial localization (semba2006biologicalfunctionsof pages 4-5). The yeast protein, lacking a mitochondrial targeting sequence, is predicted to function primarily in the cytosol.
Nit1 is highly conserved across eukaryotes, including mammals, yeast, and invertebrates, as well as in some bacteria (peracchi2017nit1isa pages 1-1). Both yeast scNit1 and mammalian Nit1 share the same primary enzymatic function as dGSH amidases (peracchi2017nit1isa pages 1-1). The evolutionary distribution of Nit1 orthologs correlates with GSH-producing organisms, underscoring the biological importance of this metabolite repair mechanism (peracchi2017nit1isa pages 8-8).
A particularly notable evolutionary feature is the NitFhit Rosetta Stone fusion protein found in invertebrates such as Drosophila melanogaster and Caenorhabditis elegans, where the Nit and Fhit (fragile histidine triad) domains are expressed as a single fused polypeptide (semba2006biologicalfunctionsof pages 1-2, semba2006biologicalfunctionsof pages 7-8). This fusion protein forms a stable tetramer with Fhit dimers on opposite poles and Nit active sites around the equator (semba2006biologicalfunctionsof pages 8-9). In mammals, Nit1 and Fhit are encoded by separate genes on different chromosomes (human chromosomes 1 and 3; mouse chromosomes 1 and 14) (semba2006biologicalfunctionsof pages 7-8). The Rosetta Stone hypothesis proposes that this fusion relationship in invertebrates predicts that the separate Nit1 and Fhit polypeptides function in the same biochemical pathway or may physically interact in mammals (semba2006biologicalfunctionsof pages 1-2). In mammals, Fhit has been characterized as a tumor suppressor, and mammalian Nit1 also exhibits tumor-suppressor-like properties, including promotion of apoptosis and suppression of cyclin D1 expression (semba2006biologicalfunctionsof pages 1-2, semba2006biologicalfunctionsof pages 4-5).
Nit1 and Nit2 are the sole representatives of branch 10 of the nitrilase superfamily (gunther2018thenitrilaseptnit1 pages 1-2, peracchi2017nit1isa pages 6-7). Despite being classified within the same branch, they have evolved distinct substrate specificities. Interestingly, phylogenetic analysis shows that enzymes acting on dGSH (dGSH amidases) and those acting on α-KGM (ω-amidases) do not form strictly separate phylogenetic clades, suggesting that substrate specialization may have arisen through convergent evolution rather than simple branching (peracchi2017nit1isa pages 6-7).
The metabolic pathway involving Nit1 can be summarized as follows: (1) Glutathione (GSH), the major intracellular antioxidant, is inadvertently acted upon by various transaminases as a minor side reaction, replacing the free amino group with a carbonyl group to form dGSH (peracchi2017nit1isa pages 1-1, peracchi2017nit1isa pages 4-5). (2) Nit1 then hydrolyzes the cyclic dGSH into α-ketoglutarate and cysteinylglycine, effectively recycling the damaged metabolite (peracchi2017nit1isa pages 1-3). Without this repair function, dGSH would be lost through excretion, potentially draining significant amounts of the cell's GSH pool and impairing antioxidant capacity (peracchi2017nit1isa pages 8-8).
This positions Nit1 not within a canonical signaling or biosynthetic pathway, but rather in a housekeeping metabolite repair pathway that protects the integrity of the glutathione pool. The broader significance of such metabolite repair enzymes is highlighted by estimates that over 600 yeast proteins (>30% of proteins of unknown function) may be enzymes whose functions remain to be determined, with metabolite damage control representing a likely function for many of them (ellens2017confrontingthecatalytic pages 1-2, ellens2017confrontingthecatalytic pages 14-15).
S. cerevisiae NIT1 (YIL164C, P40447) encodes a deaminated glutathione (dGSH) amidase — a metabolite repair enzyme belonging to branch 10 of the carbon-nitrogen hydrolase (nitrilase) superfamily. The enzyme catalyzes the hydrolysis of dGSH (a damaged form of glutathione produced by promiscuous transaminase side reactions) into α-ketoglutarate and cysteinylglycine, with a catalytic triad of Glu45-Lys127-Cys169 and remarkable substrate specificity (dGSH/α-KGM ratio of ~2400). The enzyme functions primarily in the cytoplasm and represents a conserved eukaryotic metabolite damage repair mechanism. Its biological role is to prevent the accumulation of dGSH and preserve the cellular glutathione pool.
References
(peracchi2017nit1isa pages 1-1): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 1-3): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 6-7): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 7-8): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 5-6): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 8-9): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
(peracchi2017nit1isa pages 10-10): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
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(peracchi2017nit1isa pages 4-5): Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen. Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione. Proceedings of the National Academy of Sciences, 114:E3233-E3242, Apr 2017. URL: https://doi.org/10.1073/pnas.1613736114, doi:10.1073/pnas.1613736114. This article has 65 citations and is from a highest quality peer-reviewed journal.
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(semba2006biologicalfunctionsof pages 1-2): Shuho Semba, Shuang-Yin Han, Haiyan R. Qin, Kelly A. McCorkell, Dimitrios Iliopoulos, Yuri Pekarsky, Teresa Druck, Francesco Trapasso, Carlo M. Croce, and Kay Huebner. Biological functions of mammalian nit1, the counterpart of the invertebrate nitfhit rosetta stone protein, a possible tumor suppressor*. Journal of Biological Chemistry, 281:28244-28253, Sep 2006. URL: https://doi.org/10.1074/jbc.m603590200, doi:10.1074/jbc.m603590200. This article has 69 citations and is from a domain leading peer-reviewed journal.
(semba2006biologicalfunctionsof pages 7-8): Shuho Semba, Shuang-Yin Han, Haiyan R. Qin, Kelly A. McCorkell, Dimitrios Iliopoulos, Yuri Pekarsky, Teresa Druck, Francesco Trapasso, Carlo M. Croce, and Kay Huebner. Biological functions of mammalian nit1, the counterpart of the invertebrate nitfhit rosetta stone protein, a possible tumor suppressor*. Journal of Biological Chemistry, 281:28244-28253, Sep 2006. URL: https://doi.org/10.1074/jbc.m603590200, doi:10.1074/jbc.m603590200. This article has 69 citations and is from a domain leading peer-reviewed journal.
(semba2006biologicalfunctionsof pages 8-9): Shuho Semba, Shuang-Yin Han, Haiyan R. Qin, Kelly A. McCorkell, Dimitrios Iliopoulos, Yuri Pekarsky, Teresa Druck, Francesco Trapasso, Carlo M. Croce, and Kay Huebner. Biological functions of mammalian nit1, the counterpart of the invertebrate nitfhit rosetta stone protein, a possible tumor suppressor*. Journal of Biological Chemistry, 281:28244-28253, Sep 2006. URL: https://doi.org/10.1074/jbc.m603590200, doi:10.1074/jbc.m603590200. This article has 69 citations and is from a domain leading peer-reviewed journal.
(gunther2018thenitrilaseptnit1 pages 1-2): Jan Günther, Sandra Irmisch, Nathalie D. Lackus, Michael Reichelt, Jonathan Gershenzon, and Tobias G. Köllner. The nitrilase ptnit1 catabolizes herbivore-induced nitriles in populus trichocarpa. BMC Plant Biology, Oct 2018. URL: https://doi.org/10.1186/s12870-018-1478-z, doi:10.1186/s12870-018-1478-z. This article has 24 citations and is from a peer-reviewed journal.
(ellens2017confrontingthecatalytic pages 1-2): Kenneth W. Ellens, Nils Christian, Charandeep Singh, Venkata P. Satagopam, Patrick May, and Carole L. Linster. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Research, 45:11495-11514, Oct 2017. URL: https://doi.org/10.1093/nar/gkx937, doi:10.1093/nar/gkx937. This article has 99 citations and is from a highest quality peer-reviewed journal.