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Ligand gentamicin

Basic Ligand Information

Molecular Structure

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (4 results)

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Show Natural Substrate (4 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.3.1.60

acetyl-CoA + gentamicin = CoA + N3-acetylgentamicin

756303

-

2.7.1.190

GTP + gentamicin = GDP + gentamicin 2''-phosphate

762393, 760355, 760618, 758025

-

2.7.7.46

nucleoside triphosphate + gentamicin = diphosphate + 2''-nucleotidylgentamicin

761963

-

3.5.2.6

gentamicin + H2O = ?

756142

-

Substrate in Enzyme-catalyzed Reactions (18 results)

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Show Substrate (18 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.3.1.60

acetoacetyl-CoA + gentamicin = CoA + N3'-acetoacetyl-gentamicin

706886

-

2.3.1.60

acetyl-CoA + gentamicin = CoA + N3'-acetyl-gentamicin

706886

-

2.3.1.60

acetyl-CoA + gentamicin = CoA + N3-acetylgentamicin

756303, 755693

-

2.3.1.81

4-bromo-thiophene-2-carbonyl-S-CoA + gentamicin = ?

703205

-

2.3.1.81

acetyl-CoA + gentamicin = CoA + N3'-acetyl-gentamicin

703205

-

2.3.1.81

acetyl-CoA + gentamicin = CoA + N3'-acetylgentamicin

487550, 672007, 487553

-

2.3.1.81

glycyl-CoA + gentamicin = CoA + N3'-glycyl-gentamicin

703205

-

2.3.1.81

malonyl-CoA + gentamicin = CoA + N3'-malonyl-gentamicin

703205

-

2.3.1.81

N-propionyl-CoA + gentamicin = CoA + N3'-propionyl-gentamicin

703205

-

2.3.1.82

acetyl-CoA + gentamicin = CoA + 6'-N-acetylgentamicin

701732, 735730, 755691

-

2.3.1.82

acetyl-CoA + gentamicin = CoA + N6'-acetylgentamicin

672253, 672194, 636905, 736322

-

2.3.1.82

acetyl-CoA + gentamycin = CoA + ?

755693

-

2.7.1.190

ATP + gentamicin = ADP + gentamicin 2''-phosphate

733113

-

2.7.1.190

GTP + gentamicin = GDP + gentamicin 2''-phosphate

762393, 760355, 760618, 758025

-

2.7.7.46

ATP + gentamicin = diphosphate + 2''-adenylylgentamicin

761963, 762337

-

2.7.7.46

nucleoside triphosphate + gentamicin = diphosphate + 2''-nucleotidylgentamicin

761963

-

2.3.1.60

3 entries

2.3.1.81

6 entries

2.3.1.82

3 entries

2.7.1.190

2 entries

2.7.7.46

2 entries

3.5.2.6

gentamicin + H2O = ?

756142

-

7.6.2.2

ATP + H2O + gentamicin[side 1] = ADP + phosphate + gentamicin[side 2]

746765

-

Product in Enzyme-catalyzed Reactions (1 result)

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Show Product (1 entry)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

7.6.2.2

ATP + H2O + gentamicin[side 1] = ADP + phosphate + gentamicin[side 2]

0

-

Activator in Enzyme-catalyzed Reactions (1 result)

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Show Activating Compound (1 entry)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

3.4.21.53

induces lon protease by subinhibitory concentrations

681804

-

Inhibitor in Enzyme-catalyzed Reactions (10 results)

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Show Inhibitors (10 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

1.13.12.7

induces nonsense suppression

695557

-

2.3.1.60

-

637298

-

2.3.1.82

substrate inhibition

636905

-

2.5.1.120

-

758574

-

2.7.1.6

-

704761

-

3.1.1.32

the inhibition by aminoglycosides appears to be due to substrate depletion caused by binding of aminoglycosides to the negatively charged phospholipid and can be overcome by raising the substrate concentration

94340

-

3.2.2.26

-

749468

-

3.2.2.27

-

750294

-

3.4.21.37

slight inhibition of purified elastase

664848

-

5.3.4.1

analysis of binding and dissociation constants with PDI and PDI domain deletion mutants

694931

-

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (11 results)

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Show Turnover Number (11 entries)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

2.3.1.81

0.041

-

pH 6.6, with malonyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.81

0.123

-

pH 6.6, with n-propionyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.81

0.182

-

pH 6.6, with acetyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.81

40

-

in 50 mM HEPES, pH 7.5 and 0.1 mM 4,4'-dithiodipyridine, at pH 7.8 and 25°C

672007

2.3.1.82

0.016

-

pH 8.0, 37°C

755691

2.3.1.82

0.055

-

pH 8.0, 37°C

755691

2.3.1.82

0.5

-

pH 7.5

672194

2.3.1.82

1.11

-

full length enzyme, pH 7.5, 25°C

735730

2.3.1.82

1.17

-

pH 7.5, 25°C

755693

2.3.1.82

2

-

reaction with AAC (6')-Ib' domain

672253

2.3.1.82

3.33

-

isolated AAC(6') domain, pH 7.5, 25°C

735730

2.3.1.81

4 entries

2.3.1.82

7 entries

K_M Value (14 results)

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Show KM Value (14 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.3.1.81

0.00097

-

in 50 mM HEPES, pH 7.5 and 0.1 mM 4,4'-dithiodipyridine, at pH 7.8 and 25°C

672007

2.3.1.81

0.0029

-

pH 6.6, with n-propionyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.81

0.0046

-

pH 6.6, with acetyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.81

0.0189

-

pH 6.6, with malonyl-CoA, His-tagged enzyme expressed from vector pET22b

703205

2.3.1.82

0.00504

-

full length enzyme, pH 7.5, 25°C

735730

2.3.1.82

0.0083

-

reaction with AAC (6?)-Ib' domain

672253

2.3.1.82

0.0087

-

S 0.5 value, Hill coefficient 1.84, pH 8.0, 37°C

755691

2.3.1.82

0.0143

-

isolated AAC(6') domain, pH 7.5, 25°C

735730

2.3.1.82

0.015

-

pH 7.5

672194

2.3.1.82

0.0176

-

S 0.5 value, Hill coefficient 2.05, pH 8.0, 37°C

755691

2.3.1.82

0.022

-

K 0.5 value, Hill coefficient 3.14, pH 7.5, 25°C

755693

2.3.1.82

0.077

-

pH 7.5, 37°C

636905

2.3.1.82

0.297

-

pH 6.5, 37°C

636905

2.3.1.82

0.653

-

pH 5.5, 37°C

636905

2.3.1.81

4 entries

2.3.1.82

10 entries

K_i Value (4 results)

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Show KI Value (4 entries)

EC NUMBER

KI VALUE [MM]

KI VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.3.1.60

0.16

-

-

637298

2.3.1.82

0.02256

-

pH 5.5, 37°C, substrate inhibition

636905

2.3.1.82

0.0482

-

pH 6.5, 37°C, substrate inhibition

636905

2.3.1.82

0.079

-

pH 7.5, 37°C, substrate inhibition

636905

2.3.1.82

3 entries

IC₅₀ Value (2 results)

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Show IC50 Value (2 entries)

EC NUMBER

IC50 VALUE

IC50 VALUE MAXIMUM

COMMENTARY

LITERATURE

2.7.1.6

36.6

-

-

704761

3.2.2.26

0.0021

-

at pH 7.4 and 25°C

749468

References & Links

Literature References (33)

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Show Reference (33 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

94340

10348899

Characterization of heparin low-affinity phospholipase A1 present in brain and testicular tissue

1999

Uchiyama, S.I.; Miyazaki, Y.; Amakasu, Y.; Kuwata, H.; Nakatani, Y.; Atsumi, G.I.; Murakami, M.; Kudo, I.

J. Biochem.

125

1001-1010

487550

9727487

Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase

1998

Wolf, E.; Vassilev, A.; Makino, Y.; Sali, A.; Nakatani, Y.; Burley, S.K.

Cell

94

439-449

487553

12709352

Novel 3-N-aminoglycoside acetyltransferase gene, aac(3)-Ic, from a Pseudomonas aeruginosa integron

2003

Riccio, M.L.; Docquier, J.D.; Dell'Amico, E.; Luzzaro, F.; Amicosante, G.; Rossolini, G.M.

Antimicrob. Agents Chemother.

47

1746-1748

636905

8737138

pH Modulation of aminoglycoside resistance in Staphylococcus epidermidis harboring 6'-N-aminoglycoside acetyltransferase

1996

Culebras, E.; Martinez, J.L.; Baquero, F.; Perez-Diaz, J.C.

J. Antimicrob. Chemother.

37

881-889

637298

764855

Purification and properties of gentamicin acetyltransferase I

1976

Williams, J.W.; Northrop, D.B.

Biochemistry

15

125-131

664848

12108869

Colistin stimulates the activity of neutrophil elastase and Pseudomonas aeruginosa elastase

2002

Jones, A.; Elphick, H.; Pettitt, E.; Everard, M.L.; Evans, G.S.

Eur. Respir. J.

19

1136-1141

672007

16331988

The kinetic mechanism of AAC3-IV aminoglycoside acetyltransferase from Escherichia coli

2005

Magalhaes, M.L.; Blanchard, J.S.

Biochemistry

44

16275-16283

672194

16819836

Characterization of the bifunctional aminoglycoside-modifying enzyme ANT(3)-Ii/AAC(6)-IId from Serratia marcescens

2006

Kim, C.; Hesek, D.; Zajicek, J.; Vakulenko, S.B.; Mobashery, S.

Biochemistry

45

8368-8377

672253

17417880

Mechanistic characterization of the bifunctional aminoglycoside-modifying enzyme AAC(3)-Ib/AAC(6)-Ib from Pseudomonas aeruginosa

2007

Kim, C.; Villegas-Estrada, A.; Hesek, D.; Mobashery, S.

Biochemistry

46

5270-5282

681804

17259618

The Lon protease of Pseudomonas aeruginosa is induced by aminoglycosides and is involved in biofilm formation and motility

2007

Marr, A.K.; Overhage, J.; Bains, M.; Hancock, R.E.

Microbiology

153

474-482

694931

-

Interaction of human protein disulfide isomerase and human P5 with drug compounds: Analysis using biosensor technology

2008

Horibe, T.; Kikuchi, M.; Kawakami, K.

Process Biochem.

43

1330-1337

695557

19850001

Endotoxin assay by bioluminescence Using mutant firefly luciferase

2010

Noda, K.; Goto, H.; Murakami, Y.; Ahmed, A.B.; Kuroda, A.

Anal. Biochem.

397

152-155

701732

19349516

AAC(6)-Iaf, a novel aminoglycoside 6-N-acetyltransferase from multidrug-resistant Pseudomonas aeruginosa clinical isolates

2009

Kitao, T.; Miyoshi-Akiyama, T.; Kirikae, T.

Antimicrob. Agents Chemother.

53

2327-2334

703205

19899089

Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides

2010

Green, K.D.; Chen, W.; Houghton, J.L.; Fridman, M.; Garneau-Tsodikova, S.

ChemBioChem

11

119-126

704761

19433218

Functional studies of rat galactokinase

2009

Chu, X.; Li, N.; Liu, X.; Li, D.

J. Biotechnol.

141

142-146

706886

19128900

Genetic analysis of antimicrobial resistance in Escherichia coli isolated from diarrheic neonatal calves

2009

Ahmed, A.M.; Younis, E.E.; Osman, S.A.; Ishida, Y.; El-Khodery, S.A.; Shimamoto, T.

Vet. Microbiol.

136

397-402

733113

23129050

Novel aminoglycoside 2-phosphotransferase identified in a gram-negative pathogen

2013

Toth, M.; Frase, H.; Antunes, N.T.; Vakulenko, S.B.

Antimicrob. Agents Chemother.

57

452-457

735730

23485681

Domain dissection and characterization of the aminoglycoside resistance enzyme ANT(3'')-Ii/AAC(6')-IId from Serratia marcescens

2013

Green, K.; Garneau-Tsodikova, S.

Biochimie

95

1319-1325

736322

25576529

New plasmid-mediated aminoglycoside 6-N-acetyltransferase, AAC(6')-Ian, and ESBL, TLA-3, from a Serratia marcescens clinical isolate

2015

Jin, W.; Wachino, J.; Kimura, K.; Yamada, K.; Arakawa, Y.

J. Antimicrob. Chemother.

70

1331-1337

746765

27381387

The heterodimeric ABC transporter EfrCD mediates multidrug efflux in Enterococcus faecalis

2016

Huerlimann, L.M.; Corradi, V.; Hohl, M.; Bloemberg, G.V.; Tieleman, D.P.; Seeger, M.A.

Antimicrob. Agents Chemother.

60

5400-5411

749468

30339406

Transition-state analogues of Campylobacter jejuni 5'-methylthioadenosine nucleosidase

2018

Ducati, R.G.; Harijan, R.K.; Cameron, S.A.; Tyler, P.C.; Evans, G.B.; Schramm, V.L.

ACS Chem. Biol.

13

3173-3183

750294

25435323

A label-free and sensitive fluorescent method for the detection of uracil-DNA glycosylase activity

2015

Tao, J.; Song, P.; Sato, Y.; Nishizawa, S.; Teramae, N.; Tong, A.; Xiang, Y.

Chem. Commun. (Camb.)

51

929-932

755691

27785912

Structural and biochemical characterization of Acinetobacter spp. aminoglycoside acetyltransferases highlights functional and evolutionary variation among antibiotic resistance enzymes

2017

Stogios, P.; Kuhn, M.; Evdokimova, E.; Law, M.; Courvalin, P.; Savchenko, A.

ACS Infect. Dis.

3

132-143

755693

28756664

Structural and functional survey of environmental aminoglycoside acetyltransferases reveals functionality of resistance enzymes

2017

Xu, Z.; Stogios, P.J.; Quaile, A.T.; Forsberg, K.J.; Patel, S.; Skarina, T.; Houliston, S.; Arrowsmith, C.; Dantas, G.; Savchenko, A.

ACS Infect. Dis.

3

653-665

756142

26064896

Characterization of multidrug resistant extended-spectrum beta-lactamase-producing Escherichia coli among uropathogens of pediatrics in north of Iran

2015

Rezai, M.S.; Salehifar, E.; Rafiei, A.; Langaee, T.; Rafati, M.; Shafahi, K.; Eslami, G.

BioMed Res. Int.

2015

309478

756303

31775609

N-acetyltransferase AAC(3)-I confers gentamicin resistance to Phytophthora palmivora and Phytophthora infestans

2019

Evangelisti, E.; Yunusov, T.; Shenhav, L.; Schornack, S.

BMC Microbiol.

19

265

758025

27858324

A bifunctional aminoglycoside acetyltransferase/phosphotransferase conferring tobramycin resistance provides an efficient selectable marker for plastid transformation

2017

Tabatabaei, I.; Ruf, S.; Bock, R.

Plant Mol. Biol.

93

269-281

758574

30891141

Antibacterial strategy against H. pylori Inhibition of the radical SAM enzyme MqnE in menaquinone biosynthesis

2019

Joshi, S.; Fedoseyenko, D.; Mahanta, N.; Ducati, R.G.; Feng, M.; Schramm, V.L.; Begley, T.P.

ACS Med. Chem. Lett.

10

363-366

760355

29661878

Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2'')-Ia

2018

Caldwell, S.J.; Berghuis, A.M.

Antimicrob. Agents Chemother.

62

e00202-18

760618

26802312

Aminoglycoside binding and catalysis specificity of aminoglycoside 2''-phosphotransferase IVa A thermodynamic, structural and kinetic study

2016

Kaplan, E.; Guichou, J.F.; Chaloin, L.; Kunzelmann, S.; Leban, N.; Serpersu, E.H.; Lionne, C.

Biochim. Biophys. Acta

1860

802-813

761963

30111627

Aminoglycoside heteroresistance in Acinetobacter baumannii AB5075

2018

Anderson, S.E.; Sherman, E.X.; Weiss, D.S.; Rather, P.N.

mSphere

3

e00271-18

762337

28734024

Effect of solvent and protein dynamics in ligand recognition and inhibition of aminoglycoside adenyltransferase 2''-Ia

2017

Bacot-Davis, V.R.; Bassenden, A.V.; Sprules, T.; Berghuis, A.M.

Protein Sci.

26

1852-1863

762393

-

Aminoglycoside phosphotransferase AphSR2 from Streptomyces rimosus ATCC 10970 dependence of antibiotic Resistance on serine-threonine protein kinases PkSR1 and PkSR2

2020

Rudakova, N.; Alekseeva, M.; Zakharevich, N.; Mavletova, D.; Danilenko, V.

Russ. J. Genet.

56

112-117

Links to other databases for gentamicin

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Show Links (1 entry)

ChEBI

PubChem

-