The Enzyme Database

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EC 1.7.1.13     
Accepted name: preQ1 synthase
Reaction: 7-aminomethyl-7-carbaguanine + 2 NADP+ = 7-cyano-7-carbaguanine + 2 NADPH + 2 H+
For diagram of queuine biosynthesis, click here
Glossary: 7-aminomethyl-7-carbaguanine = preQ1 = 7-aminomethyl-7-deazaguanine
7-cyano-7-carbaguanine = preQ0 = 7-cyano-7-deazaguanine
Other name(s): YkvM; QueF; preQ0 reductase; preQ0 oxidoreductase; 7-cyano-7-deazaguanine reductase; queuine synthase (incorrect as queuine is not the product); queuine:NADP+ oxidoreductase (incorrect as queuine is not the product)
Systematic name: 7-aminomethyl-7-carbaguanine:NADP+ oxidoreductase
Comments: The reaction occurs in the reverse direction. This enzyme catalyses one of the early steps in the synthesis of queuosine (Q-tRNA), and is followed by the action of EC 2.4.2.29, tRNA-guanosine34 transglycosylase. Queuosine is found in the wobble position of tRNAGUN in Eukarya and Bacteria [2] and is thought to be involved in translational modulation. The enzyme is not a GTP cyclohydrolase, as was thought previously based on sequence-homology studies.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1256460-80-6
References:
1.  Van Lanen, S.G., Reader, J.S., Swairjo, M.A., de Crécy-Lagard, V., Lee, B. and Iwata-Reuyl, D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc. Natl. Acad. Sci. USA 102 (2005) 4264–4269. [DOI] [PMID: 15767583]
2.  Yokoyama, S., Miyazawa, T., Iitaka, Y., Yamaizumi, Z., Kasai, H. and Nishimura, S. Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA. Nature 282 (1979) 107–109. [PMID: 388227]
3.  Kuchino, Y., Kasai, H., Nihei, K. and Nishimura, S. Biosynthesis of the modified nucleoside Q in transfer RNA. Nucleic Acids Res. 3 (1976) 393–398. [DOI] [PMID: 1257053]
4.  Okada, N., Noguchi, S., Nishimura, S., Ohgi, T., Goto, T., Crain, P.F. and McCloskey, J.A. Structure determination of a nucleoside Q precursor isolated from E. coli tRNA: 7-(aminomethyl)-7-deazaguanosine. Nucleic Acids Res. 5 (1978) 2289–2296. [DOI] [PMID: 353740]
5.  Noguchi, S., Yamaizumi, Z., Ohgi, T., Goto, T., Nishimura, Y., Hirota, Y. and Nishimura, S. Isolation of Q nucleoside precursor present in tRNA of an E. coli mutant and its characterization as 7-(cyano)-7-deazaguanosine. Nucleic Acids Res. 5 (1978) 4215–4223. [DOI] [PMID: 364423]
6.  Swairjo, M.A., Reddy, R.R., Lee, B., Van Lanen, S.G., Brown, S., de Crécy-Lagard, V., Iwata-Reuyl, D. and Schimmel, P. Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 61 (2005) 945–948. [DOI] [PMID: 16511203]
[EC 1.7.1.13 created 2006]
 
 
EC 1.17.99.6     
Accepted name: epoxyqueuosine reductase
Reaction: queuosine34 in tRNA + acceptor + H2O = epoxyqueuosine34 in tRNA + reduced acceptor
For diagram of queuine biosynthesis, click here
Glossary: queuine = base Q = 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydropyrrolo[3,2-e]pyrimidin-4-one
epoxyqueine = base oQ
Other name(s): oQ reductase; queG (gene name); queH (gene name)
Systematic name: queuosine34 in tRNA:acceptor oxidoreductase
Comments: This enzyme catalyses the last step in the bacterial biosynthetic pathway to queuosine, the modified guanosine base in the wobble position in tRNAs specific for Tyr, His, Asp or Asn.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miles, Z.D., McCarty, R.M., Molnar, G. and Bandarian, V. Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc. Natl. Acad. Sci. USA 108 (2011) 7368–7372. [DOI] [PMID: 21502530]
2.  Zallot, R., Ross, R., Chen, W.H., Bruner, S.D., Limbach, P.A. and De Crecy-Lagard, V. Identification of a novel epoxyqueuosine reductase family by comparative genomics. LID - 10.1021/acschembio.6b01100 [doi. ACS Chem. Biol. (2017) . [DOI] [PMID: 28128549]
[EC 1.17.99.6 created 2014]
 
 
EC 2.4.2.29     
Accepted name: tRNA-guanosine34 preQ1 transglycosylase
Reaction: guanine34 in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7-carbaguanine34 in tRNA + guanine
For diagram of queuine biosynthesis, click here
Glossary: 7-aminomethyl-7-carbaguanine = preQ1 = 7-aminomethyl-7-deazaguanine
7-cyano-7-carbaguanine = preQ0 = 7-cyano-7-deazaguanine
Other name(s): guanine insertion enzyme (ambiguous); tRNA transglycosylase (ambiguous); Q-insertase (ambiguous); transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine34 transglycosidase (ambiguous); TGT (ambiguous); transfer ribonucleic acid guanine34 transglycosylase (ambiguous)
Systematic name: tRNA-guanosine34:7-aminomethyl-7-deazaguanine tRNA-D-ribosyltransferase
Comments: Certain prokaryotic and eukaryotic tRNAs contain the modified base queuine at position 34. In eubacteria, which produce queuine de novo, the enzyme catalyses the exchange of guanine with the queuine precursor preQ1, which is ultimately modified to queuosine [5]. The enzyme can also use an earlier intermediate, preQ0, to replace guanine in unmodified tRNATyr and tRNAAsn [1]. This enzyme acts after EC 1.7.1.13, preQ1 synthase, in the queuine-biosynthesis pathway. cf. EC 2.4.2.64, tRNA-guanosine34 queuine transglycosylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72162-89-1
References:
1.  Okada, N., Noguchi, S., Kasai, H., Shindo-Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J. Biol. Chem. 254 (1979) 3067–3073. [PMID: 372186]
2.  Noguchi, S., Nishimura, Y., Hirota, Y. and Nishimura, S. Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA. J. Biol. Chem. 257 (1982) 6544–6550. [PMID: 6804468]
3.  Chong, S., Curnow, A.W., Huston, T.J. and Garcia, G.A. tRNA-guanine transglycosylase from Escherichia coli is a zinc metalloprotein. Site-directed mutagenesis studies to identify the zinc ligands. Biochemistry 34 (1995) 3694–3701. [DOI] [PMID: 7893665]
4.  Goodenough-Lashua, D.M. and Garcia, G.A. tRNA-guanine transglycosylase from E. coli: a ping-pong kinetic mechanism is consistent with nucleophilic catalysis. Bioorg. Chem. 31 (2003) 331–344. [DOI] [PMID: 12877882]
5.  Todorov, K.A. and Garcia, G.A. Role of aspartate 143 in Escherichia coli tRNA-guanine transglycosylase: alteration of heterocyclic substrate specificity. Biochemistry 45 (2006) 617–625. [DOI] [PMID: 16401090]
[EC 2.4.2.29 created 1984, modified 2007, modified 2012, modified 2020]
 
 
EC 2.4.2.64     
Accepted name: tRNA-guanosine34 queuine transglycosylase
Reaction: guanine34 in tRNA + queuine = queuine34 in tRNA + guanine
For diagram of queuine biosynthesis, click here
Glossary: queuine = base Q = 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydropyrrolo[3,2-e]pyrimidin-4-one
Other name(s): QTRT1 (gene name); QTRT2 (gene name); TGT (ambiguous); guanine insertion enzyme (ambiguous); tRNA transglycosylase (ambiguous); Q-insertase (ambiguous); queuine34 transfer ribonucleate ribosyltransferase; transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine34 transglycosidase (ambiguous); queuine tRNA-ribosyltransferase; [tRNA]-guanine34:queuine tRNA-D-ribosyltransferase; transfer ribonucleic acid guanine34 transglycosylase (ambiguous)
Systematic name: tRNA-guanosine34:queuine tRNA-D-ribosyltransferase
Comments: Certain prokaryotic and eukaryotic tRNAs contain the modified base queuine at position 34. In eukaryotes and a small number of prokaryotes queuine is salvaged and incorporated into tRNA directly via a base-exchange reaction, replacing guanine. cf. EC 2.4.2.29, tRNA-guanosine34 preQ1 transglycosylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72162-89-1
References:
1.  Howes, N.K. and Farkas, W.R. Studies with a homogeneous enzyme from rabbit erythrocytes catalyzing the insertion of guanine into tRNA. J. Biol. Chem. 253 (1978) 9082–9087. [PMID: 721832]
2.  Shindo-Okada, N., Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Transfer ribonucleic acid guanine transglycosylase isolated from rat liver. Biochemistry 19 (1980) 395–400. [DOI] [PMID: 6986171]
3.  Boland, C., Hayes, P., Santa-Maria, I., Nishimura, S. and Kelly, V.P. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J. Biol. Chem. 284 (2009) 18218–18227. [DOI] [PMID: 19414587]
4.  Yuan, Y., Zallot, R., Grove, T.L., Payan, D.J., Martin-Verstraete, I., Sepic, S., Balamkundu, S., Neelakandan, R., Gadi, V.K., Liu, C.F., Swairjo, M.A., Dedon, P.C., Almo, S.C., Gerlt, J.A. and de Crecy-Lagard, V. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc. Natl. Acad. Sci. USA 116 (2019) 19126–19135. [DOI] [PMID: 31481610]
[EC 2.4.2.64 created 2020 (EC 2.4.2.29 created 1984, modified 2007, modified 2012, part transferred 2020 to EC 2.4.2.64)]
 
 
EC 2.4.99.17     
Accepted name: S-adenosylmethionine:tRNA ribosyltransferase-isomerase
Reaction: S-adenosyl-L-methionine + 7-aminomethyl-7-carbaguanosine34 in tRNA = L-methionine + adenine + epoxyqueuosine34 in tRNA
For diagram of queuine biosynthesis, click here
Glossary: 7-aminomethyl-7-carbaguanine = preQ1 = 7-aminomethyl-7-deazaguanine
epoxyqueosine = oQ
Other name(s): QueA enzyme; queuosine biosynthesis protein QueA
Systematic name: S-adenosyl-L-methionine:7-aminomethyl-7-deazaguanosine ribosyltransferase (ribosyl isomerizing; L-methionine, adenine releasing)
Comments: The reaction is a combined transfer and isomerization of the ribose moiety of S-adenosyl-L-methionine to the modified guanosine base in the wobble position in tRNAs specific for Tyr, His, Asp or Asn. It is part of the queuosine biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Slany, R.K., Bosl, M., Crain, P.F. and Kersten, H. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 32 (1993) 7811–7817. [PMID: 8347586]
2.  Slany, R.K., Bosl, M. and Kersten, H. Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli. Biochimie 76 (1994) 389–393. [DOI] [PMID: 7849103]
3.  Kinzie, S.D., Thern, B. and Iwata-Reuyl, D. Mechanistic studies of the tRNA-modifying enzyme QueA: a chemical imperative for the use of AdoMet as a "ribosyl" donor. Org. Lett. 2 (2000) 1307–1310. [PMID: 10810734]
4.  Van Lanen, S.G. and Iwata-Reuyl, D. Kinetic mechanism of the tRNA-modifying enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). Biochemistry 42 (2003) 5312–5320. [DOI] [PMID: 12731872]
5.  Mathews, I., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Miller, M.D., Moy, K., Nigoghossian, E., Ouyang, J., Paulsen, J., Quijano, K., Reyes, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J. and Wilson, I.A. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold. Proteins 59 (2005) 869–874. [DOI] [PMID: 15822125]
6.  Grimm, C., Ficner, R., Sgraja, T., Haebel, P., Klebe, G. and Reuter, K. Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase. Biochem. Biophys. Res. Commun. 351 (2006) 695–701. [DOI] [PMID: 17083917]
[EC 2.4.99.17 created 2012]
 
 
EC 4.1.2.50     
Accepted name: 6-carboxytetrahydropterin synthase
Reaction: 7,8-dihydroneopterin 3′-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
For diagram of queuine biosynthesis, click here
Glossary: 7,8-dihydroneopterin 3′-triphosphate = 2-amino-6-[(1S,2R)-1,2-dihydroxy-3-triphosphooxypropyl]-4-oxo-2,3,7,8-tetrahydropteridine
6-carboxy-5,6,7,8-tetrahydropterin = 2-amino-4-oxo-2,3,5,6,7,8-hexahydropteridine-6-carboxylate
Other name(s): CPH4 synthase; queD (gene name); ToyB; ykvK (gene name)
Systematic name: 7,8-dihydroneopterin 3′-triphosphate acetaldehyde-lyase (6-carboxy-5,6,7,8-tetrahydropterin and triphosphate-forming)
Comments: Binds Zn2+. Isolated from the bacteria Bacillus subtilis and Escherichia coli. The reaction is part of the biosynthesis pathway of queuosine.The enzyme from Escherichia coli can also convert 6-pyruvoyl-5,6,7,8-tetrahydropterin and sepiapterin to 6-carboxy-5,6,7,8-tetrahydropterin [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cicmil, N. and Shi, L. Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 119–122. [DOI] [PMID: 18259064]
2.  McCarty, R.M., Somogyi, A. and Bandarian, V. Escherichia coli QueD is a 6-carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry 48 (2009) 2301–2303. [DOI] [PMID: 19231875]
[EC 4.1.2.50 created 2012]
 
 
EC 4.3.99.3     
Accepted name: 7-carboxy-7-deazaguanine synthase
Reaction: 6-carboxy-5,6,7,8-tetrahydropterin = 7-carboxy-7-carbaguanine + NH3
For diagram of queuine biosynthesis, click here
Glossary: 7-carboxy-7-carbaguanine = 7-carboxy-7-deazaguanine
Other name(s): 7-carboxy-7-carbaguanine synthase; queE (gene name)
Systematic name: 6-carboxy-5,6,7,8-tetrahydropterin ammonia-lyase
Comments: Requires Mg2+. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The S-adenosyl-L-methionine is catalytic as it is regenerated at the end of the reaction. The reaction is part of the biosynthesis pathway of queuosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  McCarty, R.M., Somogyi, A., Lin, G., Jacobsen, N.E. and Bandarian, V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of preQ0 from guanosine 5′-triphosphate in four steps. Biochemistry 48 (2009) 3847–3852. [DOI] [PMID: 19354300]
2.  McCarty, R.M., Krebs, C. and Bandarian, V. Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines. Biochemistry 52 (2013) 188–198. [DOI] [PMID: 23194065]
[EC 4.3.99.3 created 2012]
 
 
EC 6.3.4.20     
Accepted name: 7-cyano-7-deazaguanine synthase
Reaction: 7-carboxy-7-carbaguanine + NH3 + ATP = 7-cyano-7-carbaguanine + ADP + phosphate + H2O
For diagram of queuine biosynthesis, click here
Glossary: preQ0 = 7-cyano-7-carbaguanine = 7-cyano-7-deazaguanine
7-carboxy-7-carbaguanine = 7-carboxy-7-deazaguanine
Other name(s): preQ0 synthase; 7-cyano-7-carbaguanine synthase; queC (gene name)
Systematic name: 7-carboxy-7-carbaguanine:ammonia ligase (ADP-forming)
Comments: Binds Zn2+. The reaction is part of the biosynthesis pathway of queuosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  McCarty, R.M., Somogyi, A., Lin, G., Jacobsen, N.E. and Bandarian, V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of preQ0 from guanosine 5′-triphosphate in four steps. Biochemistry 48 (2009) 3847–3852. [DOI] [PMID: 19354300]
2.  Cicmil, N. and Huang, R.H. Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Proteins 72 (2008) 1084–1088. [DOI] [PMID: 18491386]
[EC 6.3.4.20 created 2012]
 
 


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