Histidine Triad (HIT) Superfamily


Histidine triad (HIT) enzymes are an ancient superfamily of nucleotide hydrolases and transferases that catalyse mechanistically similar but biologically distinct reactions on nucleotide‐containing substrates in pathways important for cellular growth, apoptosis, deoxyribonucleic acid, ribonucleic acid, vitamin and carbohydrate metabolism. Four branches of HIT enzymes function as nucleotide hydrolases. These enzymes include homologues and paralogues of histidine triad nucleotide‐binding protein, fragile histidine triad protein, APRATAXIN and scavenger decapping protein, which act in various cellular compartments. One diverse branch of the HIT superfamily contains nucleotide transferases and phosphorylases related to galactose‐1‐phosphate uridylyltransferase, AppppA phosphorylase, adenylylsulfate: phosphate adenylyltransferase, adenosine diphosphate‐glucose phosphorylase and VTC2, the guanosine diphosphate‐l‐galactose phosphorylase. This review provides tools to discern the identities and the probable functions of HIT enzymes from their sequences.

Key Concepts:

  • Histidine triad enzymes act on substrates containing a nucleoside monophosphate linked to distinct leaving groups.

  • HINT, FHIT, APRATAXIN and DCPS are HIT hydrolases.

  • GALT and VTC2 are HIT transferases.

  • Particular HIT enzymes are targeted to different cellular compartments to carry out their functions.

  • HIT enzymes remove nucleotide adducts from proteins and DNA and transform low‐molecular‐weight metabolites in cells.


Figure 1.

Catalysis by HIT enzymes. HIT substrates consist of nucleoside monophosphates varying in the base, 2′ substituent (X=OH or H) and leaving group (Y). In the first step, the enzymes form a covalent nucleotidylylated active site His intermediate with the α phosphate of the substrate, releasing the leaving group, YH. In the case of HIT hydrolases (branch 1, 2, 4 and 5 enzymes), the intermediate is hydrolysed to produce the nucleoside monophosphate (product 1). In the case of HIT transferases (branch 3 enzymes), the enzyme transfers the nucleoside monophosphate to a specific second substrate, containing phosphate (Z=O or a phosphate monoester substituent) to form product 2.

Figure 2.

Preferred substrates of HIT enzymes. (a) HINT substrate, AMP‐lysine residue; (b) Fhit substrate, ApppA; (c) GALT substrates, UDP‐glucose and galactose‐1‐phosphate; AppppA phosphorylase substrate, AppppA; APAT substrate, AMP‐SO4; ADP‐glucose phosphorylase substrate, ADP‐glucose; VTC2 substrate, GDP‐l‐galactose; (d) APRATAXIN substrate, 5′ adenylylated 5′ phosphorylated DNA; and (e) DCPS substrate, 7‐methyl GpppN.



Adler LN, Gomez TA, Clarke SG and Linster CL (2011) A novel GDP‐D‐glucose phosphorylase involved in quality control of the nucleoside diphosphate sugar pool in Caenorhabditis elegans and mammals. Journal of Biological Chemistry 286(24): 21511–21523. PMID: 21507950.

Ahel I, Rass U, El‐Khamisy SF et al. (2006) The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443: 713–716.

Bahaji A, Li J, Ovecka M et al. (2011) Arabidopsis thaliana mutants lacking ADP‐glucose pyrophosphorylase accumulate starch and wild‐type ADP‐glucose content: further evidence for the occurrence of important sources, other than ADP‐glucose pyrophosphorylase, of ADP‐glucose linked to leaf starch biosynthesis. Plant & Cell Physiology 52(7): 1162–1176. PMID: 21624897.

Barbier E and Wang JB (2009) Anti‐depressant and anxiolytic like behaviors in PKCI/HINT1 knockout mice associated with elevated plasma corticosterone level. BMC Neuroscience 10: 132. PMID: 19912621.

Bardaweel S, Ghosh B, Chou TF, Sadowsky MJ and Wagner CR (2011) E. coli histidine triad nucleotide binding protein 1 (ecHinT) is a catalytic regulator of D‐alanine dehydrogenase (DadA) activity in vivo. PLoS One 6(7): e20897. PMID: 21754980.

Barnes LD, Garrison PN, Siprashvili Z et al. (1996) Fhit, a putative tumor suppressor in humans, is a dinucleoside 5′, 5′″‐P‐1,P‐3‐triphosphate hydrolase. Biochemistry 35: 11529–11535.

Bieganowski P, Garrison PN, Hodawadekar SC et al. (2002) Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1 and Tfb3. Journal of Biological Chemistry 277: 10852–10860.

Bossé GD, Rüegger S, Ow MC et al. (2013) The decapping scavenger enzyme DCS‐1 controls microRNA levels in Caenorhabditis elegans. Molecular Cell 50(2): 281–287. PMID: 23541767.

Boylston J and Brenner C (2014) A knockdown with smoke model reveals Fhit as a repressor of heme oxygenase 1. Cell Cycle 13: (in press).

Brenner C (2002) Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. Biochemistry 41: 9003–9014.

Brenner C, Garrison P, Gilmour J et al. (1997) Crystal structures of Hint demonstrate that histidine triad proteins are GalT‐related nucleotide‐binding proteins. Nature Structural Biology 4: 231–238.

Bruser T, Selmer T and Dahl C (2000) ADP sulfurylase from Thiobacillus denitrificans is an adenylylsulfate: phosphate adenylyltransferase and belongs to a new family of nucleotidyltransferases. Journal of Biological Chemistry 275: 1691–1698.

Chen Q, Wang X, O'Neill FA et al. (2008) Is the histidine triad nucleotide‐binding protein 1 (HINT1) gene a candidate for schizophrenia? Schizophrenia Research 106(2–3): 200–207. PMID: 18799291.

Chou TF and Wagner CR (2007) Lysyl‐tRNA synthetase‐generated lysyl‐adenylate is a substrate for histidine triad nucleotide binding proteins. Journal of Biological Chemistry 282(7): 4719–4727. PMID: 17158446.

Clements PM, Breslin C, Deeks ED et al. (2004) The ataxia‐oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. DNA Repair (Amst) 3: 1493−1502.

Conklin PL, Saracco SA, Norris SR and Last RL (2000) Identification of ascorbic acid‐deficient Arabidopsis thaliana mutants. Genetics 154: 847–856.

Date H, Onodera O, Tanaka H et al. (2001) Early onset ataxia with ocular motor apraxia and hypoalbuminemia is caused by mutations in a new HIT superfamily gene. Nature Genetics 29: 184−188.

Draganescu A, Hodawadekar SC, Gee KR and Brenner C (2000) Fhit‐nucleotide specificity probed with novel fluorescent and fluorogenic substrates. Journal of Biological Chemistry 275(7): 4555–4560. PMID: 10671479.

Frey PA (1996) The Leloir pathway: a mechanistic imperative for three enzymes to change the stereochemical configuration of a single carbon in galactose. FASEB Journal 10: 461–470.

Gu M, Fabrega C, Liu SW et al. (2004) Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity. Molecular Cell 14: 67–80.

Ishii H, Vecchione A, Fong LY et al. (2004) Cancer prevention and therapy in a preclinical mouse model: impact of FHIT viruses. Current Gene Therapy 4: 53–63.

Itzen A, Blankenfeldt W and Goody RS (2011) Adenylylation: renaissance of a forgotten post‐translational modification. Trends in Biochemical Sciences 36(4): 221–228. PMID: 21256032.

Jackson KJ, Chen Q, Chen J et al. (2011) Association of the histidine‐triad nucleotide‐binding protein‐1 (HINT1) gene variants with nicotine dependence. Pharmacogenomics Journal 11(4): 251–257. PMID: 20514075.

Jackson KJ, Wang JB, Barbier E, Chen X and Damaj MI (2012) Acute behavioral effects of nicotine in male and female HINT1 knockout mice. Genes, Brain and Behavior. doi:10.1111/j.1601‐183X.2012.00827.x. PMID: 22827509.

Krakowiak A, Pace HC, Blackburn GM et al. (2004) Biochemical, crystallographic, and mutagenic characterization of hint, the AMP‐lysine hydrolase, with novel substrates and inhibitors. Journal of Biological Chemistry 279(18): 18711–18716. PMID: 14982931.

Lee YN, Nechushtan H, Figov N and Razin E (2004) The function of lysyl‐tRNA synthetase and Ap4A as signaling regulators of MITF activity in FcepsilonRI‐activated mast cells. Immunity 20: 145–151.

Linster CL, Adler LN, Webb K et al. (2008) A second GDP‐L‐galactose phosphorylase in arabidopsis en route to vitamin C. Covalent intermediate and substrate requirements for the conserved reaction. Journal of Biological Chemistry 283(27): 18483–18492. PMID: 18463094.

Linster CL, Gomez TA, Christensen KC et al. (2007) Arabidopis VTC2 encodes GDP‐l‐galactose phosphorylase, the last unknown enzyme in the Smirnoff‐Wheeler pathway to ascorbic acid in plants. Journal of Biological Chemistry 282: 18879–18885.

Liu H, Rodgers ND, Jiao X and Kiledjian M (2002) The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO Journal 21: 4699–4708.

Luo H, Chan DW, Yang T et al. (2004) A new XRCC1‐containing complex and its role in cellular survival of methyl methanesulfonate treatment. Molecular and Cellular Biology 24: 8356–8365.

Martin J, Magnino F, Schmidt K et al. (2006) Hint2, a mitochondrial apoptotic sensitizer down‐regulated in hepatocellular carcinoma. Gastroenterology 130: 2179–2188.

Martin J, Maurhofer O, Bellance N et al. (2013) Disruption of the histidine triad nucleotide‐binding hint2 gene in mice affects glycemic control and mitochondrial function. Hepatology 57(5): 2037–2048. PMID: 22961760.

McCoy JG, Arabshahi A, Bitto E et al. (2006) Structure and mechanism of an ADP‐glucose phosphorylase from Arabidopsis thaliana. Biochemistry 45: 3154–3162.

Miuma S, Saldivar JC, Karras JR et al. (2013) Fhit deficiency‐induced global genome instability promotes mutation and clonal expansion. PLoS One 8(11): e80730. PMID: 24244712.

Moreira MC, Barbot C, Tachi N et al. (2001) The gene mutated in ataxia‐ocular apraxia 1 encodes the new HIT/Zn‐finger protein aprataxin. Nature Genetics 29: 189–193.

Nagai H, Sezaki M, Bertocchini F, Fukuda K and Sheng G (2014) HINTW, a W‐chromosome HINT gene in chick, is expressed ubiquitously and is a robust female cell marker applicable in intraspecific chimera studies. Genesis 52(5): 424–430. PMID: 24599776.

Pace HC, Hodawadekar SC, Draganescu A et al. (2000) Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers. Current Biology 10: 907–917.

Parks KP, Seidle H, Wright N et al. (2004) Altered specificity of Hint‐W123Q supports a role for Hint inhibition by Asw in avian sex determination. Physiological Genomics 20: 12–14.

Plateau P, Fromant M, Schmitter JM and Blanquet S (1990) Catabolism of bis(5′‐nucleosidyl) tetraphosphates in Saccharomyces cerevisiae. Journal of Bacteriology 172: 6892–6899.

Reijns MA, Rabe B, Rigby RE et al. (2012) Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149(5): 1008–1022. PMID: 22579044.

Robu ME, Larson JD, Nasevicius A et al. (2007) p53 Activation by knockdown technologies. PLoS Genetics 3(5): e78.

Rubio‐Texeira M, Varnum JM, Bieganowski P and Brenner C (2002) Control of dinucleoside polyphosphates by the FHIT‐homologous HNT2 gene, adenine biosynthesis and heat shock in Saccharomyces cerevisiae. BMC Molecular Biology 3: 7.

Seidle HF, Bieganowski P and Brenner C (2005) Disease‐associated mutations inactivate AMP‐lysine hydrolase activity of Aprataxin. Journal of Biological Chemistry 280: 20927–20931.

Smith CA, Roeszler KN and Sinclair AH (2009) Genetic evidence against a role for W‐linked histidine triad nucleotide binding protein (HINTW) in avian sex determination. International Journal of Developmental Biology 53(1): 59–67. PMID: 19123127.

Su T, Suzui M, Wang L et al. (2003) Deletion of histidine triad nucleotide‐binding protein 1/PKC‐interacting protein in mice enhances cell growth and carcinogenesis. Proceedings of the National Academy of Sciences of the USA 100: 7824–7829.

Trapasso F, Krakowiak A, Cesari R et al. (2003) Designed FHIT alleles establish that Fhit‐induced apoptosis in cancer cells is limited by substrate‐binding. Proceedings of the National Academy of Sciences of the USA 100: 1592–1597.

Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA and Williams RS (2014) Aprataxin resolves adenylated RNA‐DNA junctions to maintain genome integrity. Nature 506(7486): 111–115. PMID: 24362567.

Varadarajulu J, Lebar M, Krishnamoorthy G et al. (2011) Increased anxiety‐related behaviour in Hint1 knockout mice. Behavioural Brain Research 220(2): 305–311. PMID: 21316396.

Wang Z, Jiao X, Carr‐Schmid A and Kiledjian M (2002) The hDcp2 protein is a mammalian mRNA decapping enzyme. Proceedings of the National Academy of Sciences of the USA 99: 12663–12668.

Weiske J and Huber O (2005) The histidine triad protein Hint1 interacts with Pontin and Reptin and inhibits TCF‐beta‐catenin‐mediated transcription. Journal of Cell Science 118: 3117–3129.

Zimoń M, Baets J, Almeida‐Souza L et al. (2012) Loss‐of‐function mutations in HINT1 cause axonal neuropathy with neuromyotonia. Nature Genetics 44(10): 1080–1083. PMID: 22961002.

Further Reading

Bianchi F, Tagliabue E, Ménard S and Campiglio M (2007) Fhit expression protects against HER2‐driven breast tumor development: unraveling the molecular interconnections. Cell Cycle 6(6): 643–646.

Calderon FR, Phansalkar AR, Crockett DK, Miller M and Mao R (2007) Mutation database for the galactose‐1‐phosphate uridyltransferase (GALT) gene. Human Mutation 28(10): 939–943.

Chen N, Walsh MA, Liu Y, Parker R and Song H (2005) Crystal structures of human DcpS in ligand‐free and m7GDP‐bound forms suggest a dynamic mechanism for scavenger mRNA decapping. Journal of Molecular Biology 347(4): 707–718.

Rass U, Ahel I and West SC (2007) Actions of aprataxin in multiple DNA repair pathways. Journal of Biological Chemistry 282(13): 9469–9474.

Wang L, Zhang Y, Li H et al. (2007) Hint1 inhibits growth and activator protein‐1 activity in human colon cancer cells. Cancer Research 67(10): 4700–4708.

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Brenner, Charles(Aug 2014) Histidine Triad (HIT) Superfamily. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020545.pub2]