The Enzyme Database

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EC 1.1.3.43     
Accepted name: paromamine 6′-oxidase
Reaction: paromamine + O2 = 6′-dehydroparomamine + H2O2
Other name(s): btrQ (gene name); neoG (gene name); kanI (gene name); tacB (gene name); neoQ (obsolete gene name)
Systematic name: paromamine:oxygen 6′-oxidoreductase
Comments: Contains FAD. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Works in combination with EC 2.6.1.93, neamine transaminase, to replace the 6′-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces fradiae also catalyses EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.  Yu, Y., Hou, X., Ni, X. and Xia, H. Biosynthesis of 3′-deoxy-carbamoylkanamycin C in a Streptomyces tenebrarius mutant strain by tacB gene disruption. J. Antibiot. (Tokyo) 61 (2008) 63–69. [DOI] [PMID: 18408324]
3.  Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]
[EC 1.1.3.43 created 2012]
 
 
EC 2.3.1.81     
Accepted name: aminoglycoside 3-N-acetyltransferase
Reaction: acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N3-acetyl-2-deoxystreptamine antibiotic
For diagram of neamine and ribostamycin biosynthesis, click here
Glossary: kanamycin
Other name(s): 3-aminoglycoside acetyltransferase; 3-N-aminoglycoside acetyltransferase; aminoglycoside N3-acetyltransferase; acetyl-CoA:2-deoxystreptamine-antibiotic N3′-acetyltransferase (incorrect); aminoglycoside N3′-acetyltransferase (incorrect)
Systematic name: acetyl-CoA:2-deoxystreptamine-antibiotic N3-acetyltransferase
Comments: Different from EC 2.3.1.60 gentamicin 3-N-acetyltransferase. A wide range of antibiotics containing the 2-deoxystreptamine ring can act as acceptors, including gentamicin, kanamycin, tobramycin, neomycin and apramycin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 60120-42-5
References:
1.  Davies, J. and O'Connor, S. Enzymatic modification of aminoglycoside antibiotics: 3-N-Acetyltransferase with broad specificity that determines resistance to the novel aminoglycoside apramycin. Antimicrob. Agents Chemother. 14 (1978) 69–72. [PMID: 356726]
[EC 2.3.1.81 created 1984, modified 2015]
 
 
EC 2.4.1.301     
Accepted name: 2′-deamino-2′-hydroxyneamine 1-α-D-kanosaminyltransferase
Reaction: (1) UDP-α-D-kanosamine + 2′-deamino-2′-hydroxyneamine = UDP + kanamycin A
(2) UDP-α-D-kanosamine + neamine = UDP + kanamycin B
(3) UDP-α-D-kanosamine + paromamine = UDP + kanamycin C
(4) UDP-α-D-kanosamine + 2′-deamino-2′-hydroxyparomamine = UDP + kanamycin X
For diagram of kanamycin A biosynthesis, click here
Glossary: neamine = (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-α-D-glucopyranoside
paromamine = (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2-deoxy-α-D-glucopyranoside
UDP-α-D-kanosamine = uridine 5′-[3-(3-amino-3-deoxy-α-D-glucopyranosyl) diphosphate]
kanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
kanamycin B = (1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-α-D-glucopyranoside
kanamycin C = (1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2-amino-2-deoxy-α-D-glucopyranoside
kanamycin X = (1S,2R,3R,4S,6R)-4,6-diamino-3-(α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
Other name(s): kanE (gene name); kanM2 (gene name)
Systematic name: UDP-α-D-kanosamine:2′-deamino-2′-hydroxyneamine 1-α-D-kanosaminyltransferase
Comments: Involved in the biosynthetic pathway of kanamycins. The enzyme characterized from the bacterium Streptomyces kanamyceticus can also accept UDP-α-D-glucose with lower efficiency [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kudo, F., Sucipto, H. and Eguchi, T. Enzymatic activity of a glycosyltransferase KanM2 encoded in the kanamycin biosynthetic gene cluster. J. Antibiot. (Tokyo) 62 (2009) 707–710. [DOI] [PMID: 19911031]
2.  Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]
[EC 2.4.1.301 created 2013]
 
 
EC 2.4.2.49     
Accepted name: neamine phosphoribosyltransferase
Reaction: neamine + 5-phospho-α-D-ribose 1-diphosphate = 5′′-phosphoribostamycin + diphosphate
For diagram of neamine and ribostamycin biosynthesis, click here
Glossary: neamine = (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}oxane-3,4-diol
ribostamycin = (2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2-{[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxycyclohexyl]oxy}oxane-3,4-diol
Other name(s): btrL (gene name); neoM (gene name)
Systematic name: neamine:5-phospho-α-D-ribose 1-diphosphate phosphoribosyltransferase
Comments: Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including ribostamycin, neomycin and butirosin. The enzyme requires a divalent metal ion, optimally Mg2+, Ni2+ or Co2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kudo, F., Fujii, T., Kinoshita, S. and Eguchi, T. Unique O-ribosylation in the biosynthesis of butirosin. Bioorg. Med. Chem. 15 (2007) 4360–4368. [DOI] [PMID: 17482823]
[EC 2.4.2.49 created 2013]
 
 
EC 2.6.1.93     
Accepted name: neamine transaminase
Reaction: neamine + 2-oxoglutarate = 6′-dehydroparomamine + L-glutamate
For diagram of neamine and ribostamycin biosynthesis, click here
Other name(s): glutamate—6′-dehydroparomamine aminotransferase; btrB (gene name); neoN (gene name); kacL (gene name)
Systematic name: neamine:2-oxoglutarate aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin B, butirosin, neomycin and ribostamycin. Works in combination with EC 1.1.3.43, paromamine 6-oxidase, to replace the 6′-hydroxy group of paromamine with an amino group. The enzyme from the bacterium Streptomyces kanamyceticus can also catalyse EC 2.6.1.94, 2′-deamino-2′-hydroxyneamine transaminase, which leads to production of kanamycin A [3]. The enzyme from the bacterium Streptomyces fradiae can also catalyse EC 2.6.1.95, leading to production of neomycin C [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.  Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]
3.  Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]
[EC 2.6.1.93 created 2012]
 
 
EC 2.6.1.94     
Accepted name: 2′-deamino-2′-hydroxyneamine transaminase
Reaction: 2′-deamino-2′-hydroxyneamine + 2-oxoglutarate = 2′-deamino-2′-hydroxy-6′-dehydroparomamine + L-glutamate
Other name(s): kacL (gene name)
Systematic name: 2′-deamino-2′-hydroxyneamine:2-oxoglutarate aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of kanamycin A and kanamycin D. The enzyme, characterized from the bacterium Streptomyces kanamyceticus, can also catalyse EC 2.6.1.93, neamine transaminase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [DOI] [PMID: 21983602]
[EC 2.6.1.94 created 2012]
 
 
EC 2.6.1.95     
Accepted name: neomycin C transaminase
Reaction: neomycin C + 2-oxoglutarate = 6′′′-deamino-6′′′-oxoneomycin C + L-glutamate
Other name(s): neoN (gene name)
Systematic name: 2-oxoglutarate:neomycin C aminotransferase
Comments: The reaction occurs in vivo in the opposite direction. Involved in the biosynthetic pathway of aminoglycoside antibiotics of the neomycin family. Works in combination with EC 1.1.3.44, 6′′′-hydroxyneomycin C oxidase, to replace the 6′′′-hydroxy group of 6′′′-deamino-6′′′-hydroxyneomycin C with an amino group. The enzyme, characterized from the bacterium Streptomyces fradiae, can also catalyse EC 2.6.1.93, neamine transaminase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Huang, F., Spiteller, D., Koorbanally, N.A., Li, Y., Llewellyn, N.M. and Spencer, J.B. Elaboration of neosamine rings in the biosynthesis of neomycin and butirosin. ChemBioChem 8 (2007) 283–288. [DOI] [PMID: 17206729]
2.  Clausnitzer, D., Piepersberg, W. and Wehmeier, U.F. The oxidoreductases LivQ and NeoQ are responsible for the different 6′-modifications in the aminoglycosides lividomycin and neomycin. J. Appl. Microbiol. 111 (2011) 642–651. [DOI] [PMID: 21689223]
[EC 2.6.1.95 created 2012]
 
 
EC 2.7.1.95     
Accepted name: kanamycin kinase
Reaction: ATP + kanamycin = ADP + kanamycin 3′-phosphate
Glossary: kanamycin
Other name(s): neomycin-kanamycin phosphotransferase;
Systematic name: ATP:kanamycin 3′-O-phosphotransferase
Comments: Also acts on the antibiotics neomycin, paromomycin, neamine, paromamine, vistamycin and gentamicin A. An enzyme from Pseudomonas aeruginosa also acts on butirosin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 62213-36-9
References:
1.  Doi, O., Ogura, M., Tanaka, N. and Umezawa, H. Inactivation of kanamycin, neomycin, and streptomycin by enzymes obtained in cells of Pseudomonas aeruginosa. Appl. Microbiol. 16 (1968) 1276–1281. [PMID: 4970990]
2.  Dolin, M.I. The Streptococcus faecalis oxidases for reduced diphosphopyridine nucleotide. III. Isolation and properties of a flavin peroxidase for reduced diphosphopyridine nucleotide. J. Biol. Chem. 225 (1957) 557–573. [PMID: 13416259]
[EC 2.7.1.95 created 1976]
 
 
EC 3.1.3.88     
Accepted name: 5′′-phosphoribostamycin phosphatase
Reaction: 5′′-phosphoribostamycin + H2O = ribostamycin + phosphate
For diagram of neamine and ribostamycin biosynthesis, click here
Other name(s): btrP (gene name); neoI (gene name)
Systematic name: 5′′-phosphoribostamycin phosphohydrolase
Comments: Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including ribostamycin, neomycin and butirosin. No metal is required for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kudo, F., Fujii, T., Kinoshita, S. and Eguchi, T. Unique O-ribosylation in the biosynthesis of butirosin. Bioorg. Med. Chem. 15 (2007) 4360–4368. [DOI] [PMID: 17482823]
[EC 3.1.3.88 created 2012]
 
 


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