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 2.4.2.29     
Accepted name: tRNA-guanosine34 transglycosylase
Reaction: (1) guanine34 in tRNA + queuine = queuine34 in tRNA + guanine
(2) 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
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): guanine insertion enzyme (ambiguous); tRNA transglycosylase (ambiguous); Q-insertase (ambiguous); queuine34 transfer ribonucleate ribosyltransferase; transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine34 transglycosidase; queuine tRNA-ribosyltransferase (ambiguous); TGT; [tRNA]-guanine34:queuine tRNA-D-ribosyltransferase; transfer ribonucleic acid guanine34 transglycosylase
Systematic name: tRNA-guanosine34:queuine tRNA-D-ribosyltransferase
Comments: Certain prokaryotic and eukaryotic tRNAs contain the modified base queuine at position 34. In eukaryotes queuine is salvaged from food and incorporated into tRNA directly via a base-exchange reaction, replacing guanine. 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 [4,5]. The eubacterial enzyme can also use an earlier intermediate, preQ0, to replace guanine in unmodified tRNATyr and tRNAAsn [2]. This enzyme acts after EC 1.7.1.13, preQ1 synthase, in the queuine-biosynthesis pathway.
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.  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]
3.  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. [PMID: 6986171]
4.  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]
5.  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]
[EC 2.4.2.29 created 1984, modified 2007, modified 2012]
 
 
EC 2.4.2.48     
Accepted name: tRNA-guanine15 transglycosylase
Reaction: guanine15 in tRNA + 7-cyano-7-carbaguanine = 7-cyano-7-carbaguanine15 in tRNA + guanine
Glossary: 7-cyano-7-carbaguanine = preQ0 = 7-cyano-7-deazaguanine
archaeosine = G* = 7-amidino-7-deazaguanosine
Other name(s): tRNA transglycosylase (ambiguous); transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine15 transglycosidase; TGT (ambiguous); transfer ribonucleic acid guanine15 transglycosylase
Systematic name: tRNA-guanine15:7-cyano-7-carbaguanine tRNA-D-ribosyltransferase
Comments: Archaeal tRNAs contain the modified nucleoside archaeosine at position 15. This archaeal enzyme catalyses the exchange of guanine at position 15 of tRNA with the base preQ0, which is ultimately modified to form the nucleoside archaeosine (cf. EC 2.6.1.97) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Bai, Y., Fox, D.T., Lacy, J.A., Van Lanen, S.G. and Iwata-Reuyl, D. Hypermodification of tRNA in thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii. J. Biol. Chem. 275 (2000) 28731–28738. [DOI] [PMID: 10862614]
[EC 2.4.2.48 created 2012]
 
 
EC 2.6.1.97     
Accepted name: archaeosine synthase
Reaction: L-glutamine + 7-cyano-7-carbaguanine15 in tRNA + H2O = L-glutamate + archaeine15 in tRNA
Glossary: 7-cyano-7-carbaguanine = preQ0 = 7-cyano-7-deazaguanine
archaeine = 7-deaza-7-carbamidoylguanine = base G*
archaeosine = G* = 7-amidino-7-deazaguanosine
Other name(s): ArcS; TgtA2; MJ1022 (gene name); glutamine:preQ0-tRNA amidinotransferase (incorrect)
Systematic name: L-glutamine:7-cyano-7-carbaguanine aminotransferase
Comments: In Euryarchaeota the reaction is catalysed by ArcS [1,2]. In Crenarchaeota, which do not have an ArcS homologue, the reaction is catalysed either by a homologue of EC 6.3.4.20, 7-cyano-7-deazaguanine synthase that includes a glutaminase domain (cf. EC 3.5.1.2), or by a homologue of EC 1.7.1.13, preQ1 synthase [2]. The enzyme from the Euryarchaeon Methanocaldococcus jannaschii can also use arginine and ammonium as amino donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Phillips, G., Chikwana, V.M., Maxwell, A., El-Yacoubi, B., Swairjo, M.A., Iwata-Reuyl, D. and de Crecy-Lagard, V. Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. J. Biol. Chem. 285 (2010) 12706–12713. [DOI] [PMID: 20129918]
2.  Phillips, G., Swairjo, M.A., Gaston, K.W., Bailly, M., Limbach, P.A., Iwata-Reuyl, D. and de Crecy-Lagard, V. Diversity of archaeosine synthesis in crenarchaeota. ACS Chem. Biol. 7 (2012) 300–305. [DOI] [PMID: 22032275]
[EC 2.6.1.97 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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