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Ligand D-methionine

Basic Ligand Information

Molecular Structure

Show all BRENDA pathways known for D-methionine

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (7 results)

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Show Natural Substrate (7 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.4.3.3

D-Met + H2O + O2 = 4-methylthio-2-oxobutanoate + NH3 + H2O2

743827

-

1.4.3.3

D-methionine + H2O + O2 = 4-methylsulfanyl-2-oxobutanoate + NH3 + H2O2

711306, 711547

-

1.4.3.3

D-methionine + H2O + O2 = 4-methylthio-2-oxobutanoic acid + NH3 + H2O2

391828, 391830, 391849, 391860, 391865, 391840, 391853, 391833, 391844, 391852, 391861, 391841, 391864, 391839, 391847, 391848

-

1.4.3.3

3 entries

2.3.1.36

acetyl-CoA + D-methionine = CoA + N-acetyl-D-methionine

486807

-

2.6.1.21

D-methionine + 2-oxoglutarate = 4-methylsulfanyl-2-oxobutanoate + D-glutamate

759235

-

2.6.1.41

D-methionine + pyruvate = 4-methylthio-2-oxobutanoate + L-alanine

636704

-

5.1.1.10

D-Met = L-Met

744003

-

In Vivo Product in Enzyme-catalyzed Reactions (3 results)

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Show Natural Product (3 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

3.5.1.81

N-acetyl-D-methionine + H2O = acetate + D-methionine

0

-

5.1.1.10

L-Methionine = D-Methionine

0

-

7.4.2.11

ATP + H2O + D-methionine-[methionine-binding protein][side 1] = ADP + phosphate + D-methionine[side 2] + [methionine-binding protein][side 1]

0

-

Substrate in Enzyme-catalyzed Reactions (40 results)

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Show Substrate (40 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.4.3.1

D-Met + H2O + O2 = 4-(methylsulfonyl)-2-oxobutanoate + NH3 + H2O2

742805

-

1.4.3.1

D-methionine + H2O + O2 = 4-(methylsulfonyl)-2-oxobutanoic acid + NH3 + H2O2

684383

-

1.4.3.1

D-methionine + H2O + O2 = ?

673583

-

1.4.3.19

D-methionine + H2O + O2 = 4-(methylsulfanyl)-2-oxobutanoic acid + NH3 + H2O2

689934, 701114, 698957

-

1.4.3.19

D-methionine + H2O + O2 = ?

687878

-

1.4.3.3

D-Met + H2O + O2 = 4-methylthio-2-oxobutanoate + NH3 + H2O2

672703, 674365, 743827, 743863, 675459, 391705, 654786, 741626, 741688

-

1.4.3.3

D-Met + H2O + O2 = 4-methylthio-2-oxobutanoic acid + NH3 + H2O2

724401

-

1.4.3.3

D-methionine + 2,6-dichloroindophenol = 4-methylsulfanyl-2-oxobutanoate + reduced 2,6-dichloroindophenol

711306

-

1.4.3.3

D-methionine + 2,6-dichlorophenolindophenol + H2O = ?

685713

-

1.4.3.3

D-methionine + 2,6-dichlorophenolindophenol = ?

675459

-

1.4.3.3

D-methionine + H2O + 2,6-dichloroindophenol = ?

696959

-

1.4.3.3

D-methionine + H2O + O2 = 2-oxo-4-methylthiobutyric acid + NH3 + H2O2

726525

-

1.4.3.3

D-methionine + H2O + O2 = 4-methylsulfanyl-2-oxobutanoate + NH3 + H2O2

711306, 711547, 763732

-

1.4.3.3

D-methionine + H2O + O2 = 4-methylthio-2-oxobutanoate + NH3 + H2O2

684409

-

1.4.3.3

D-methionine + H2O + O2 = 4-methylthio-2-oxobutanoic acid + NH3 + H2O2

391828, 391830, 391849, 391860, 391865, 687145, 391840, 391853, 391833, 391844, 391852, 391861, 687891, 391841, 391864, 391839, 391847, 391848, 671491, 685045, 686020, 684598, 685750, 686277, 724793

-

1.4.5.1

D-methionine + oxidized 2,6-dichloroindophenol + H2O = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichloroindophenol

394968, 394971

-

1.4.5.1

D-methionine + oxidized 2,6-dichlorophenolindophenol + H2O = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichlorophenolindophenol

696481

-

1.4.5.1

D-methionine + oxidized acceptor + H2O = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced acceptor

700217

-

1.4.99.6

D-Met + H2O + oxidized 2,6-dichlorophenolindophenol = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichlorophenolindophenol

695533

-

1.4.99.6

D-methionine + H2O + 2,6-dichlorophenolindophenol = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced 2,6-dichlorophenolindophenol

394974

-

1.4.99.6

D-methionine + H2O + iodonitrotetrazolium chloride = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced iodonitrotetrazolium chloride

705583

-

1.4.99.6

D-methionine + phenazine methosulfate + H2O = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced phenazine methosulfate

762668

-

1.4.99.6

D-methionine + phenazine methosulfate = 4-methylsulfanyl-2-oxobutanoate + NH3 + reduced phenazine methosulfate

733215, 733326

-

1.4.3.1

3 entries

1.4.3.19

2 entries

1.4.3.3

10 entries

1.4.5.1

3 entries

1.4.99.6

5 entries

1.4.99.B4

D-methionine + acceptor + acceptor = ?

764324

-

2.3.1.36

acetyl-CoA + D-methionine = CoA + N-acetyl-D-methionine

657695, 486807

-

2.3.2.12

GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Ala4 + D-methionine = GlcNAc-MurNGlyc-L-Ala1-D-iGln2-meso-DapNH23-D-Met4 + D-alanine

735442

-

2.5.1.6

ATP + D-methionine + H2O = S-adenosyl-D-methionine + phosphate + diphosphate

639074

6wkb, 3D-view

2.6.1.21

D-methionine + 2-oxoglutarate = 4-methylsulfanyl-2-oxobutanoate + D-glutamate

759235, 636736, 636738, 636742, 636746

-

2.6.1.21

D-methionine + pyruvate = 4-methylsulfanyl-2-oxobutanoate + D-alanine

759259

-

2.6.1.21

D-methionine + pyruvate = 4-methylsulfanyl-2-oxobutanoate + L-alanine

636736, 636738, 636742, 636746

-

2.6.1.41

D-methionine + 2-oxoglutarate = 4-methylthio-2-oxobutanoate + L-glutamate

636703, 636704

-

2.6.1.41

D-methionine + oxaloacetate = 4-methylthio-2-oxobutanoate + L-aspartate

636703, 636704

-

2.6.1.41

D-methionine + pyruvate = 4-methylthio-2-oxobutanoate + L-alanine

636703, 636704

-

2.6.1.21

3 entries

2.6.1.41

3 entries

2.6.1.74

D-methionine + 2-oxoadipate = 4-methylsulfanyl-2-oxobutanoate + 2-aminoadipate

640195

-

3.5.1.81

Formate + D-Met = N-Formyl-D-Met + H2O

31917

-

5.1.1.10

D-Met = L-Met

705194, 745414, 744003, 701839

-

5.1.1.10

D-methionine = L-methionine

744003, 745414, 746725

-

5.1.1.10

2 entries

5.1.1.21

D-methionine = L-methionine

729935

-

6.3.2.4

ATP + D-Ala + D-Met = ADP + phosphate + D-Ala-D-Met

1228, 1233

-

6.3.2.4

ATP + D-Met = ADP + phosphate + D-Met-D-Met

672685

-

6.3.2.4

2 entries

Product in Enzyme-catalyzed Reactions (16 results)

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Show Product (16 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.4.1.16

4-methylthio-2-oxobutanoate + NH3 + NADPH + H+ = D-methionine + NADP+

0

-

3.1.1.43

D-methionine methyl ester + H2O = D-methionine + methanol

80934, 80936, 651785

-

3.4.11.19

L-methionine amide + H2O = D-methionine + NH3

0

-

3.5.1.77

N-carbamoyl-D-Met + H2O = D-Met + NH3 + CO2

0

-

3.5.1.81

N-Acetyl-D-Met + H2O = acetate + D-Met

0

-

3.5.1.81

N-Benzoyl-D-Met + H2O = Benzoate + D-Met

0

-

3.5.1.81

N-Benzyloxycarbonyl-D-Met + H2O = Benzyloxycarbonate + D-Met

0

-

3.5.1.81

N-acetyl-D-methionine + H2O = acetate + D-methionine

0

-

3.5.1.81

N-acetyl-DL-methionine + H2O = acetate + D-methionine

0

-

3.5.1.81

5 entries

5.1.1.1

L-Methionine = D-Methionine

0

-

5.1.1.10

L-Met = D-Met

2040, 0

-

5.1.1.10

L-Methionine = D-Methionine

0

-

5.1.1.10

2 entries

5.1.1.2

L-Methionine = D-Methionine

2054

-

5.1.1.21

L-Methionine = D-Methionine

0

-

5.1.1.9

L-Met = D-Met

0, 2165

-

7.4.2.11

ATP + H2O + D-methionine-[methionine-binding protein][side 1] = ADP + phosphate + D-methionine[side 2] + [methionine-binding protein][side 1]

0

-

Activator in Enzyme-catalyzed Reactions (4 results)

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Show Activating Compound (4 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

2.6.1.54

stimulation, 127% of non-stimulated activity

637633

-

3.4.13.18

enhances activity at 0-20 mM

679283

-

3.4.13.9

the activity of isozyme prolidase I against Gly-L-Pro is strongly enhanced by D-methionine

695528

-

3.4.13.9

the activity of isozyme prolidase II against L-Met-L-Pro is enhanced by D-methionine

695528

-

3.4.13.9

2 entries

Inhibitor in Enzyme-catalyzed Reactions (12 results)

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Show Inhibitors (12 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

1.13.12.3

competitive inhibition

439347

-

1.4.1.13

19% inhibition at 50 mM

391438

-

1.4.1.20

10 mM, 25% inhibition

349634

-

1.4.1.20

10 mM, 63% inhibition

349634

-

1.4.1.20

2 entries

2.1.1.12

-

485144

-

2.3.1.46

slight feed-back inhibition

487045

-

2.5.1.6

-

639046

6wkb, 3D-view

2.6.1.21

inhibition of D- and L-transamination of D-alanine to 2-oxoglutarate, weak

636737

-

4.1.1.57

-

4721

-

4.1.1.57

i.e. (2R)-Met

4725

-

4.1.1.57

2 entries

6.1.1.10

-

58

-

7.4.2.11

92% residual activity at 5 mM with L-methionine as substrate, 23% residual activity at 50 mM with D-methionine as substrate

749753

-

3D Structure of Enzyme-Ligand-Complex (PDB) (3 results)

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Show 3D Structure of Enzyme-Ligand-Complex (PDB) (3 entries)

EC NUMBER

ENZYME 3D STRUCTURE

2.5.1.6

6wkb, 3D-view

3.4.11.18

1kq0, 3D-view

3.5.1.98

6wi3, 3D-view

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (29 results)

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Show Turnover Number (29 entries)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

1.4.3.1

4

-

mutant enzyme H56N, at pH 7.5 and 37°C

742805

1.4.3.1

11.5

-

mutant enzyme H56A, at pH 7.5 and 37°C

742805

1.4.3.3

0.84

-

recombinant mutant C108S, pH 7.5, 37°C, with 6-dichloroindophenolate

711306

1.4.3.3

1.33

-

mutant enzyme I223D/Y224G

674365

1.4.3.3

1.38

-

mutant enzymeY224G

674365

1.4.3.3

1.5

-

recombinant wild-type enzyme, pH 7.5, 37°C, with 6-dichloroindophenolate

711306

1.4.3.3

2.5

-

mutant enzyme G222D/Y224G

674365

1.4.3.3

2.8

-

recombinant mutant C108D, pH 7.5, 37°C, with 6-dichloroindophenolate

711306

1.4.3.3

6.83

-

wild-type enzyme

674365

1.4.3.3

9

-

mutant enzyme R221D/Y224G

674365

1.4.3.3

10.5

-

mutant enzyme E220D/Y224G

674365

1.4.3.3

42

-

mutant enzyme F258S, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

47.5

-

mutant Y228F

391860

1.4.3.3

63

-

mutant enzyme F258A, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

75

-

recombinant mutant C108D, pH 7.5, 37°C, with O2

711306

1.4.3.3

80.5

-

wild type enzyme, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

89

-

mutant enzyme F258Y, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

92

-

mutant Y224F

391860

1.4.3.3

110

-

recombinant mutant C108S, pH 7.5, 37°C, with O2

711306

1.4.3.3

120

-

pH 8, 55°C

763732

1.4.3.3

143

-

wild-type

391860

1.4.3.3

200

-

recombinant wild-type enzyme, pH 7.5, 37°C, with O2

711306

1.4.3.3

680

-

pH 8.5, 25°C, mutant enzyme M213R

391705

1.4.3.3

4600

-

pH 8.5, 25°C, wild-type enzyme

391705

1.4.3.1

2 entries

1.4.3.3

22 entries

1.4.5.1

16

-

-

394971

1.4.99.6

6.8

-

-

705583

1.4.99.6

154

-

pH 8.7, 25°C

733326, 762668

1.4.99.6

190

-

wild-type, pH-independent limiting value at high pH, pH not specified in the publication, temperature not specified in the publication

733215

1.4.99.6

3 entries

1.4.99.B4

0.057

-

pH 9.0, 30°C, acceptor: phenazine methosulfate/p-iodonitrotetrazolium violet

764324

K_M Value (53 results)

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Show KM Value (53 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

1.4.3.1

8.5

-

mutant enzyme H56A, at pH 7.5 and 37°C

742805

1.4.3.1

31.8

-

mutant enzyme H56N, at pH 7.5 and 37°C

742805

1.4.3.3

0.2

-

pH 8.5, 25°C, wild-type enzyme

391705

1.4.3.3

0.21

-

pH 8, 55°C

763732

1.4.3.3

0.24

-

-

391840

1.4.3.3

0.27

-

-

391847

1.4.3.3

0.29

-

-

391848

1.4.3.3

0.3

-

mutant enzyme T60A/Q144R/K152E, apparent value, at 25°C and pH 8.5

687891

1.4.3.3

0.4

-

pH 8.3, 37°C, mutant enzyme F42C

672703

1.4.3.3

0.46

-

wild type enzyme, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

0.6

-

wild type enzyme, apparent value, at 25°C and pH 8.5

687891

1.4.3.3

0.65

-

wild-type enzyme

674365

1.4.3.3

0.67

-

mutant enzyme E220D/Y224G

674365

1.4.3.3

0.67

-

mutant enzyme R221D/Y224G

674365

1.4.3.3

0.76

-

-

391846

1.4.3.3

0.8

-

mutant enzyme M213G, apparent value, at 25°C and pH 8.5

687891

1.4.3.3

0.81

-

-

391865

1.4.3.3

0.83

-

-

391828, 391833

1.4.3.3

0.9

-

pH 8.3, 37°C, wild-type enzyme

672703

1.4.3.3

1.2

-

mutant enzyme M213R, apparent value, at 25°C and pH 8.5

687891

1.4.3.3

1.5

-

pH 8.5, 25°C, mutant enzyme M213R

391705

1.4.3.3

2.9

-

mutant enzyme F258A, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

2.96

-

at pH 8.0 and 37°C

741626

1.4.3.3

3.3

-

mutant enzyme F258S, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

4.2

-

mutant enzyme F258Y, in 50 mM potassium phosphate buffer, pH 8.0, at 30°C

724401

1.4.3.3

15.6

-

mutant Y224F

391860

1.4.3.3

27.4

-

-

391853

1.4.3.3

50

-

mutant Y228F

391860

1.4.3.3

143

-

wild-type

391860

1.4.3.1

2 entries

1.4.3.3

27 entries

1.4.5.1

11

-

with 2,6-dichlorophenolindophenol

394971

1.4.99.6

1.43

-

-

705583

1.4.99.6

10

-

pH 8.7, 25°C

733326, 762668

1.4.99.6

2 entries

1.4.99.B4

2

3

pH 9.0, 30°C, acceptor: phenazine methosulfate/p-iodonitrotetrazolium violet

764324

2.5.1.6

3.5

-

-

639074

5.1.1.10

1.6

-

-

2045

5.1.1.10

2

3

crude lyophilisates, 30°C, pH 7, Vmax: 2075 micromol/min/g

705194

5.1.1.10

4.8

-

100% aqueous

672716

5.1.1.10

7.86

-

pH 7.0, 80°C

745414

5.1.1.10

7.86

-

pH 7.0, 80°C, recombinant enzyme

745414

5.1.1.10

9

-

10% methanol

672716

5.1.1.10

9.5

-

-

2049

5.1.1.10

11.1

-

10% acetonitril

672716

5.1.1.10

11.9

-

40% acetonitril

672716

5.1.1.10

13.2

-

20% acetonitril

672716

5.1.1.10

15.8

-

20% methanol

672716

5.1.1.10

22

-

crude lyophilisates, 25°C, pH 7, Vmax: 1892 micromol/min/g

705194

5.1.1.10

24.3

-

40% methanol

672716

5.1.1.10

25

-

crude lyophilisates, 20°C, pH 7, Vmax: 1696 micromol/min/g

705194

5.1.1.10

28

-

crude lyophilisates, 25°C, pH 8, Vmax: 3627 micromol/min/g

705194

5.1.1.10

30

-

crude lyophilisates, 35°C, pH 7, Vmax: 2512 micromol/min/g

705194

5.1.1.10

32

-

crude lyophilisates, 40°C, pH 7, Vmax: 2668 micromol/min/g

705194

5.1.1.10

42

-

crude lyophilisates, 25°C, pH 6, Vmax: 1160 micromol/min/g

705194

5.1.1.10

18 entries

6.3.2.4

9

-

-

1228

K_i Value (1 result)

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Show KI Value (1 entry)

EC NUMBER

KI VALUE [MM]

KI VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.5.1.6

0.4

-

-

639046

References & Links

Literature References (107)

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Show Reference (107 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

58

14693

Sulphur metabolism in Paracoccus denitrificans. Purification, properties and regulation of cysteinyl- and methionyl-tRNA synthetase

1977

Burnell, J.N.; Whatley, F.R.

Biochim. Biophys. Acta

481

266-278

1228

7893688

Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis

1995

Shi, Y.; Walsh, C.T.

Biochemistry

34

2768-2776

1233

1998664

Identification of vancomycin resistance protein VanA as a D-alanine:D-alanine ligase of altered substrate specificity

1991

Bugg, T.D.H.; Dutka-Malen, S.; Athur, M.; Courvalin, P.; Walsh, C.T.

Biochemistry

30

2017-2021

2040

5788493

Crystalline amino acid racemase with low substrate specificity

1969

Soda, K.; Osumi, T.

Biochem. Biophys. Res. Commun.

35

363-368

2045

-

Purification and characterization of amino acid racemase with very broad substrate specificity from Aeromonas caviae

1987

Inagaki, K.; Tanizawa, K.; Tanaka, H.; Soda, K.

Agric. Biol. Chem.

51

173-180

2049

-

Amino acid racemase with broad substrate specificity, its properties and use in phenylalanine racemization

1988

Asano, Y.; Endo, K.

Appl. Microbiol. Biotechnol.

29

523-527

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11948

764324

29191113

Characterization of cis-4-hydroxy-D-proline dehydrogenase from Sinorhizobium meliloti

2018

Watanabe, S.; Morimoto, D.; Fukumori, F.; Watanabe, Y.

Biosci. Biotechnol. Biochem.

82

110-113

Links to other databases for D-methionine

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ChEBI

PubChem