# GNMT

## Overview
Glycine N-methyltransferase (GNMT) is a gene that encodes the enzyme glycine N-methyltransferase, a critical enzyme involved in methionine metabolism and the regulation of methyl group homeostasis. The GNMT enzyme, primarily expressed in the liver, catalyzes the transfer of a methyl group from S-adenosylmethionine (SAM) to glycine, forming S-adenosylhomocysteine (SAH) and sarcosine. This reaction is pivotal in maintaining the balance of SAM and SAH within cells, which is essential for numerous methylation reactions. Structurally, GNMT is a tetrameric enzyme composed of identical subunits, each featuring a complex arrangement of alpha-helices and beta-strands that facilitate its enzymatic function. The enzyme's role extends beyond its catalytic activity; it also interacts with various proteins, influencing critical cellular pathways and processes, including those related to tumorigenesis and cell survival. Given its significant functions and interactions, GNMT is also studied for its implications in liver health and disease, particularly in conditions like hepatocellular carcinoma and liver steatosis (Huang2000Mechanisms; Wang2011Glycine-N).

## Structure
The human Glycine N-methyltransferase (GNMT) protein is a tetrameric enzyme, meaning its quaternary structure consists of four identical subunits. Each subunit is approximately spherical and organized into three domains: the N-terminal domain, the C-terminal domain, and the S-domain. The C-terminal domain binds AdoMet/AdoHcy and includes a consensus peptide folding, while the S-domain comprises an alpha-helix, a large loop, and three antiparallel beta-strands. The N-terminal domain features a beta-strand, a large loop (U-loop), and an alpha-helix (Huang2000Mechanisms).

The secondary structure of GNMT includes nine alpha-helices and 11 beta-strands per subunit, contributing to the stability and functional specificity of the enzyme (Huang2000Mechanisms). The tertiary structure is characterized by the arrangement of these helices and strands in a three-dimensional space, crucial for the enzyme's catalytic activity. The quaternary structure, as a tetramer, allows for cooperative interactions between subunits, essential for the sequential binding and release of substrates and products (Huang2000Mechanisms).

Post-translational modifications of GNMT include phosphorylation, with several phosphorylated serine residues identified in the rat GNMT, such as Ser9, Ser71, Ser139, Ser182, and Ser241. These modifications likely regulate the enzyme's activity and interactions (Luka2008Chapter). The enzyme's structure and function are highly conserved across different species, as evidenced by the similarity in amino acid sequences and structural features (Luka2003Effect).

## Function
Glycine N-methyltransferase (GNMT) is an enzyme that plays a critical role in methionine metabolism and methyl group homeostasis within the liver. It is involved in the conversion of S-adenosylmethionine (SAM) to S-adenosylhomocysteine (SAH), while simultaneously generating sarcosine from glycine. This conversion is crucial as it helps regulate the SAM:SAH ratio, essential for cellular methylation reactions (Wang2011Glycine-N). GNMT expression affects transmethylation kinetics and SAM synthesis, facilitating the conservation of methyl groups by limiting homocysteine remethylation fluxes (Wang2011Glycine-N).

In addition to its role in methylation, GNMT is involved in folate-mediated one-carbon metabolism, crucial for DNA synthesis and repair. It acts as a folate binding protein, promoting methylene-folate dependent pyrimidine synthesis and formyl-folate dependent purine synthesis, particularly in hepatocellular carcinoma (HCC) (Chen2022Downregulation). GNMT also plays a protective role in cellular defense against DNA damage by enhancing nucleotide biosynthesis and reducing uracil misincorporation in DNA, thereby improving DNA integrity and potentially preventing human cancer (Chen2022Downregulation).

Furthermore, GNMT has been identified as a potential tumor suppressor, often inactivated in human hepatoma. Its proper function is crucial for preventing methyl deficiency, which can promote tumorigenesis (Wang2011Glycine-N). GNMT's expression and activity are linked to folate retention and bioavailability in the liver, indicating its importance in metabolic processes (Chen2022Downregulation).

## Clinical Significance
Mutations in the GNMT gene, which encodes glycine N-methyltransferase, have been linked to various liver diseases, including hepatocellular carcinoma (HCC) and mild to moderate liver disease. Deficiencies in GNMT are associated with elevated serum aminotransferases, a marker of liver damage, and can lead to the development of liver steatosis, fibrosis, and HCC, particularly noted in experimental studies with GNMT-knockout mice (Martínez-Chantar2007Loss). In humans, mutations such as the 3415A>G change resulting in an Asn140Ser substitution significantly reduce GNMT activity, impacting methionine metabolism and leading to isolated persistent hypermethioninemia and elevated plasma AdoMet (Augoustides‐Savvopoulou2003Glycine).

Furthermore, the loss of GNMT gene expression is commonly observed in patients at risk of developing HCC, such as those with hepatitis C virus and alcohol-induced cirrhosis, suggesting a critical role of GNMT in liver health beyond genetic mutations (Martínez-Chantar2007Loss). The gene's down-regulation is also implicated in the progression of liver diseases in various patient populations, indicating a broader clinical significance (Varela-Rey2010Fatty).

Additionally, GNMT deficiency, an autosomal recessive disorder, has been associated with mild to moderate fluctuating elevations of aminotransferases and hepatomegaly, although it typically lacks overt symptoms. This condition underscores the importance of GNMT in liver function and its potential role as a tumor-susceptibility gene for liver cancer (Barić2016Consensus).

## Interactions
Glycine N-methyltransferase (GNMT) interacts with several proteins, influencing various cellular pathways and processes. One significant interaction is with DEP domain containing 6 (DEPDC6), also known as DEPTOR. This interaction, identified through yeast two-hybrid screening and confirmed by immunoprecipitation and FRET-AB assays, involves the C-terminal half of GNMT binding to the PDZ domain of DEPTOR. This binding affects the mTOR signaling pathway, crucial for cell growth and survival, and has implications in hepatocellular carcinoma (HCC) where GNMT acts as a tumor suppressor (Yen2011Functional).

Additionally, GNMT interacts with PREX2, a PTEN inhibitor involved in the PTEN/PI3K/AKT signaling pathways. This interaction, facilitated by the PDZ domains of PREX2, was demonstrated through in vitro immunoprecipitation assays. GNMT's interaction with PREX2 leads to the degradation of PREX2 through the ubiquitination pathway mediated by the E3 ligase HectH9, affecting the AKT signaling pathway known for promoting cell proliferation and survival (Li2017Characterization).

These interactions highlight GNMT's role in regulating key signaling pathways that influence cell proliferation, survival, and tumorigenesis, underscoring its potential as a therapeutic target in diseases like HCC.


## References


[1. (Huang2000Mechanisms) Yafei Huang, Junichi Komoto, Kiyoshi Konishi, Yoshimi Takata, Hirofumi Ogawa, Tomoharu Gomi, Motoji Fujioka, and Fusao Takusagawa. Mechanisms for auto-inhibition and forced product release in glycine n-methyltransferase: crystal structures of wild-type, mutant r175k and s-adenosylhomocysteine-bound r175k enzymes. Journal of Molecular Biology, 298(1):149–162, April 2000. URL: http://dx.doi.org/10.1006/jmbi.2000.3637, doi:10.1006/jmbi.2000.3637. (41 citations) 10.1006/jmbi.2000.3637](https://doi.org/10.1006/jmbi.2000.3637)

[2. (Yen2011Functional) Chia-Hung Yen, Yao-Cheng Lu, Chung-Hsien Li, Cheng-Ming Lee, Chia-Yen Chen, Ming-Yuan Cheng, Shiu-Feng Huang, Kuen-Feng Chen, Ann-Lii Cheng, Li-Ying Liao, Yan-Hwa Wu Lee, and Yi-Ming Arthur Chen. Functional characterization of glycine n-methyltransferase and its interactive protein depdc6/deptor in hepatocellular carcinoma. Molecular Medicine, 18(2):286–296, December 2011. URL: http://dx.doi.org/10.2119/molmed.2011.00331, doi:10.2119/molmed.2011.00331. (64 citations) 10.2119/molmed.2011.00331](https://doi.org/10.2119/molmed.2011.00331)

[3. (Wang2011Glycine-N) Yi-Cheng Wang, Feng-Yao Tang, Shih-Yin Chen, Yi-Ming Chen, and En-Pei Isabel Chiang. Glycine-n methyltransferase expression in hepg2 cells is involved in methyl group homeostasis by regulating transmethylation kinetics and dna methylation1,2. The Journal of Nutrition, 141(5):777–782, May 2011. URL: http://dx.doi.org/10.3945/jn.110.135954, doi:10.3945/jn.110.135954. (45 citations) 10.3945/jn.110.135954](https://doi.org/10.3945/jn.110.135954)

[4. (Augoustides‐Savvopoulou2003Glycine) P. Augoustides‐Savvopoulou, Z. Luka, S. Karyda, S. P. Stabler, R. H. Allen, K. Patsiaoura, C. Wagner, and S. H. Mudd. Glycine n‐methyltransferase deficiency: a new patient with a novel mutation. Journal of Inherited Metabolic Disease, 26(8):745–759, December 2003. URL: http://dx.doi.org/10.1023/b:boli.0000009978.17777.33, doi:10.1023/b:boli.0000009978.17777.33. (68 citations) 10.1023/b:boli.0000009978.17777.33](https://doi.org/10.1023/b:boli.0000009978.17777.33)

[5. (Li2017Characterization) Chung-Hsien Li, Chia-Hung Yen, Yen-Fu Chen, Kuo-Jui Lee, Cheng-Chieh Fang, Xian Zhang, Chih-Chung Lai, Shiu-Feng Huang, Hui-Kuan Lin, and Yi-Ming Arthur Chen. Characterization of the gnmt-hecth9-prex2 tripartite relationship in the pathogenesis of hepatocellular carcinoma: gnmt regulates prex2 level via hecth9. International Journal of Cancer, 140(10):2284–2297, March 2017. URL: http://dx.doi.org/10.1002/ijc.30652, doi:10.1002/ijc.30652. (29 citations) 10.1002/ijc.30652](https://doi.org/10.1002/ijc.30652)

[6. (Luka2008Chapter) Zigmund Luka. Chapter 11 Methyltetrahydrofolate in Folate‐Binding Protein Glycine N‐Methyltransferase, pages 325–345. Elsevier, 2008. URL: http://dx.doi.org/10.1016/s0083-6729(08)00411-1, doi:10.1016/s0083-6729(08)00411-1. (20 citations) 10.1016/s0083-6729(08)00411-1](https://doi.org/10.1016/s0083-6729(08)00411-1)

[7. (Luka2003Effect) Zigmund Luka and Conrad Wagner. Effect of naturally occurring mutations in human glycine n-methyltransferase on activity and conformation. Biochemical and Biophysical Research Communications, 312(4):1067–1072, December 2003. URL: http://dx.doi.org/10.1016/j.bbrc.2003.11.037, doi:10.1016/j.bbrc.2003.11.037. (21 citations) 10.1016/j.bbrc.2003.11.037](https://doi.org/10.1016/j.bbrc.2003.11.037)

[8. (Martínez-Chantar2007Loss) M. Luz Martínez-Chantar, Mercedes Vázquez-Chantada, Usue Ariz, Nuria Martínez, Marta Varela, Zigmund Luka, Antonieta Capdevila, Juan Rodríguez, Ana M. Aransay, Rune Matthiesen, Heping Yang, Diego F. Calvisi, Manel Esteller, Mario Fraga, Shelly C. Lu, Conrad Wagner, and José M. Mato. Loss of the glycine n-methyltransferase gene leads to steatosis and hepatocellular carcinoma in mice. Hepatology, 47(4):1191–1199, December 2007. URL: http://dx.doi.org/10.1002/hep.22159, doi:10.1002/hep.22159. (239 citations) 10.1002/hep.22159](https://doi.org/10.1002/hep.22159)

[9. (Varela-Rey2010Fatty) Marta Varela-Rey, Nuria Martínez-López, David Fernández-Ramos, Nieves Embade, Diego F. Calvisi, Aswhin Woodhoo, Juan Rodríguez, Mario F. Fraga, Josep Julve, Elisabeth Rodríguez-Millán, Itziar Frades, Luís Torres, Zigmund Luka, Conrad Wagner, Manel Esteller, Shelly C. Lu, M. Luz Martínez-Chantar, and José M. Mato. Fatty liver and fibrosis in glycine n-methyltransferase knockout mice is prevented by nicotinamide. Hepatology, 52(1):105–114, March 2010. URL: http://dx.doi.org/10.1002/hep.23639, doi:10.1002/hep.23639. (96 citations) 10.1002/hep.23639](https://doi.org/10.1002/hep.23639)

[10. (Barić2016Consensus) Ivo Barić, Christian Staufner, Persephone Augoustides‐Savvopoulou, Yin‐Hsiu Chien, Dries Dobbelaere, Sarah C. Grünert, Thomas Opladen, Danijela Petković Ramadža, Bojana Rakić, Anna Wedell, and Henk J. Blom. Consensus recommendations for the diagnosis, treatment and follow‐up of inherited methylation disorders. Journal of Inherited Metabolic Disease, 40(1):5–20, September 2016. URL: http://dx.doi.org/10.1007/s10545-016-9972-7, doi:10.1007/s10545-016-9972-7. (65 citations) 10.1007/s10545-016-9972-7](https://doi.org/10.1007/s10545-016-9972-7)

[11. (Chen2022Downregulation) Po-Ming Chen, Cheng-Hsueh Tsai, Chieh-Cheng Huang, Hau-Hsuan Hwang, Jian-Rong Li, Chun-Chi Liu, Hsin-An Ko, and En-Pei Isabel Chiang. Downregulation of methionine cycle genes mat1a and gnmt enriches protein-associated translation process and worsens hepatocellular carcinoma prognosis. International Journal of Molecular Sciences, 23(1):481, January 2022. URL: http://dx.doi.org/10.3390/ijms23010481, doi:10.3390/ijms23010481. (12 citations) 10.3390/ijms23010481](https://doi.org/10.3390/ijms23010481)