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Ligand D-cycloserine

Basic Ligand Information

Molecular Structure

Related pathways

Show all BRENDA pathways known for D-cycloserine

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Roles as Enzyme Ligand

In Vivo Product in Enzyme-catalyzed Reactions (2 results)

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Show Natural Product (2 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

6.3.3.5

O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + ammonia + ADP + phosphate

-

-

6.3.3.5

O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + NH3 + ADP + phosphate

-

-

6.3.3.5

2 entries

Substrate in Enzyme-catalyzed Reactions (3 results)

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Show Substrate (3 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

1.4.3.3

D-cycloserine + H2O + O2 = ? + NH3 + H2O2

763089

-

1.4.5.1

D-cycloserine + oxidized 2,6-dichloroindophenol + H2O = ?

696481

-

6.3.2.4

D-cycloserine = ?

662288, 662904

-

Product in Enzyme-catalyzed Reactions (3 results)

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Show Product (3 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

6.3.3.5

beta-aminooxy-D-alanine + ATP + H2O = D-cycloserine + ?

-

-

6.3.3.5

O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + ammonia + ADP + phosphate

-

-

6.3.3.5

O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + NH3 + ADP + phosphate

-

-

6.3.3.5

3 entries

Inhibitor in Enzyme-catalyzed Reactions (60 results)

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Show Inhibitors (60 entries)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

1.13.11.88

1 mM, 48% loss of activity

749754

-

2.1.2.1

-

441393, 441403, 441408, 441410, 441411, 441420, 441427

-

2.1.2.1

interaction extreme rapidly and irreversible

441416

-

2.1.2.1

overexpression of SHMT-S increases resistance in a rich folate containing medium

675874

-

2.1.2.1

3 entries

2.3.1.47

-

487052, 755744

-

2.5.1.144

18% residual activity at 5 mM

637347

-

2.5.1.47

82% loss of activity at 5 mM

637347

-

2.5.1.48

-

637439

-

2.6.1.113

-

739832

-

2.6.1.14

weak

637254

-

2.6.1.19

-

637043, 637056, 637059

-

2.6.1.21

-

636738, 636742

-

2.6.1.21

0.000025 mM, 50% inhibition

636737

-

2.6.1.21

2 entries

2.6.1.37

1 mM, 40% inhibition

636706

-

2.6.1.40

-

644426

-

2.6.1.42

DCS, mechanism-based inhibition of the Mycobacterium tuberculosis branched-chain aminotransferase by D-cycloserine, mechanism and enzyme-bound three-dimensional structure with a role of residue C196, overview. Time and concentration-dependent inactivation. The structure of the covalent D-cycloserine-PMP adduct bound to MtIlvE reveals that the D-cycloserine ring is planar and aromatic

758558

-

2.6.1.44

DCS, commercialized as Seromycin, a reversible inhibitor of AGT. DCS displays a time-dependent binding mainly generating an oxime intermediate, inhibition mechanism, overview

758763

-

2.6.1.55

0.5 mM; 20% inhibition

636678, 636679

-

2.6.1.62

-

637090

-

2.8.1.7

inhibitor of PLP-dependent enzymes, inhibits CPSIT_0959 protein catalytic activity

761583

-

3.5.5.5

weak

32503

-

3.7.1.3

-

289270

-

3.7.1.3

1 mM

289263

-

4.1.1.64

-

4750

-

4.1.1.64

competitive, L-isomer has 3000fold greater inhibitory potency than D-isomer

652809

-

3.7.1.3

2 entries

4.1.1.64

2 entries

4.1.2.26

1 mM, 98% inhibition

663708

-

4.3.1.15

-

6046

-

4.8.1.2

35% inhibition at 0.1 mM in the absence of Na2S

763288

-

5.1.1.1

-

716705

1XQL, 3D-view

5.1.1.1

-

672649, 673726, 675672, 676977, 695001, 716705, 747417, 748310

1XQL, 3D-view

5.1.1.1

1 mM, 95% inhibition

650876

1XQL, 3D-view

5.1.1.1

active site bound inhibitor, binding structure, overview

746615

1XQL, 3D-view

5.1.1.1

an alanine racemase inhibitor

726834

1XQL, 3D-view

5.1.1.1

competitive inhibition, importance of N2-structural site in cyloserine for bioactivity

748310

1XQL, 3D-view

5.1.1.1

competitive inhibitor, importance of N2-structural site in cyloserine for bioactivity

748310

1XQL, 3D-view

5.1.1.1

DCS, inhibits enzyme Alr irreversibly by covalently bonding to pyridoxal 5'-phosphate, molecular modeling

746767

1XQL, 3D-view

5.1.1.1

importance of N2-structural site in cyloserine for bioactivity

748310

1XQL, 3D-view

5.1.1.1

mechanism of inactivation and comparison with inactivation of Bacillus stearothermophilus enzyme

662289

1XQL, 3D-view

5.1.1.1

mechanism of inactivation and comparison with inactivation of Streptomyces lavendulae enzyme

662289

1XQL, 3D-view

5.1.1.1

model for inactivation mechanism via geminal diamine and ketimine to isoxazole

661196

1XQL, 3D-view

5.1.1.1

specific inhibition is reversible by D-alanine in the growth medium

728258

1XQL, 3D-view

5.1.1.1

structural features such as the hinge angle or the surface area between the monomers do not contribute to D-cycloserine resistance, binding structure analysis, overview

746985

1XQL, 3D-view

5.1.1.1

time-dependent inactivation rate of enzyme from Streptomyces lavendulae is slower than for enzyme from Escherichia coli

662288

1XQL, 3D-view

5.1.1.1

time-dependent inactivation rate of enzyme from Streptomyces lavendulae is slower than for enzyme from Escherichia coli. Enzyme from Streptomyces lavendulae is one of its self-resistance determinants

662288

1XQL, 3D-view

5.1.1.1

16 entries

5.1.1.10

-

2041, 2049

-

5.1.1.13

-

650892

-

5.1.1.15

-

2088

-

5.1.1.15

21% inhibition at 1 mM

748352

-

5.1.1.15

2 entries

5.1.1.17

1 mM, 23% inhibition

492260

-

5.1.1.18

2 mM, 64% inhibition

662887

-

6.3.2.4

-

745681

-

6.3.2.4

-

1227, 1230, 1233, 1234, 1235, 1236, 662288, 662904, 745534, 770422, 770936, 771050, 771465, 774731

-

6.3.2.4

0.2 mg/ml, approx. 50% inhibition, 0.8 mg/ml, approx. 80% inhibition

649337

-

6.3.2.4

0.2 mg/ml, approx. 60% inhibition, 0.8 mg/ml, approx. 95% inhibition

649337

-

6.3.2.4

a competitive inhibitor

745827

-

6.3.2.4

a slow-onset inhibitor specifically to the Mycobacterium tuberculosis enzyme orthologue, inhibition mechanism, overview. D-Cycloserine binds exclusively to the C-terminal D-alanine binding site, even in the absence of bound D-alanine at the N-terminal binding site

727032

-

6.3.2.4

competitive inhibitor

691244

-

6.3.2.4

interferes with the formation of peptidoglycan biosynthesis by competitive inhibition of alanine racemase and D-alanine-D-alanine ligase, the latter is the primary lethal target, inhibition mechanism and physiological effects, NMR metabolomic study, overview. D-Alanine is able to effectively compete with the inhibitor for uptake

728209

-

6.3.2.4

preferential and weak inhibition at the second, lower-affinity binding site. D-cycloserine binding is tighter at higher ATP concentrations

713773

-

6.3.2.4

weak inhibition

652963

-

6.3.2.4

10 entries

Metals and Ions (1 result)

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Show Metals Ions (1 entry)

EC NUMBER

COMMENTARY

LITERATURE

ENZYME 3D STRUCTURE

4.8.1.2

the enzyme activity is increased 1.6fold at 0.1 mM D-cycloserine in the presence of Na2S

763288

-

3D Structure of Enzyme-Ligand-Complex (PDB) (1 result)

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Show 3D Structure of Enzyme-Ligand-Complex (PDB) (1 entry)

EC NUMBER

ENZYME 3D STRUCTURE

5.1.1.1

1XQL, 3D-view

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (1 result)

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Show Turnover Number (1 entry)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

1.4.3.3

0.77

-

pH 8.5, 25°C

763089

K_M Value (2 results)

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Show KM Value (2 entries)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

1.4.3.3

83.5

-

pH 8.5, 25°C

763089

1.4.5.1

200

-

-

696481

K_i Value (17 results)

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Show KI Value (17 entries)

EC NUMBER

KI VALUE [MM]

KI VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.1.2.1

2.02

-

-

441408

2.1.2.7

0.002

-

-

485776

2.1.2.7

0.0022

-

-

485777

2.1.2.7

2 entries

2.6.1.21

0.000011

-

pH 8.0, 37°C

636742

5.1.1.1

0.0086

-

pH and temperature not specified in the publication

748310

5.1.1.1

0.0138

-

pH and temperature not specified in the publication

748310

5.1.1.1

0.073

-

pH and temperature not specified in the publication

748310

5.1.1.1

0.086

-

in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication

716705

5.1.1.1

0.33

-

mutant Y265F, 37°C, pH 9.1

661196

5.1.1.1

0.87

-

pH 8.2, 25°C

662288

5.1.1.1

1.2

-

pH 8.2, 25°C

662288

5.1.1.1

4

-

or higher, wild-type, 37°C, pH 9.1

661196

6.3.2.4

0.002

-

-

662904

6.3.2.4

0.106559

-

competitive inhibition with respect to ATP, at pH 8.0 and 37°C

771465

6.3.2.4

0.182108

-

competitive inhibition with respect to D-alanine, at pH 8.0 and 37°C

771465

6.3.2.4

0.185

-

-

691244

6.3.2.4

0.92

-

-

662288

5.1.1.1

8 entries

6.3.2.4

5 entries

IC₅₀ Value (10 results)

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Show IC50 Value (10 entries)

EC NUMBER

IC50 VALUE

IC50 VALUE MAXIMUM

COMMENTARY

LITERATURE

5.1.1.1

0.0054

-

pH 11.0, 35°C, recombinant His-tagged enzyme

747417

5.1.1.1

0.0264

-

wild-type enzyme, pH and temperature not specified in the publication

746767

5.1.1.1

0.058

-

in 100 mM Tris-Tricine, pH 8.5, temperature not specified in the publication

716705

5.1.1.1

0.65

-

pH and temperature not specified in the publication

748310

5.1.1.1

0.712

-

enzyme mutant R373L, pH and temperature not specified in the publication

746767

5.1.1.1

1.328

-

enzyme mutant Y364D, pH and temperature not specified in the publication

746767

6.3.2.4

0.00098

-

at pH 8.0 and 30°C

771050

6.3.2.4

0.025

-

at pH 7.4, temperature not specified in the publication

770936

6.3.2.4

0.276

-

at pH 8.0 and 37°C

774731

6.3.2.4

0.37

-

pH not specified in the publication, temperature not specified in the publication

713773

5.1.1.1

6 entries

6.3.2.4

4 entries

References & Links

Literature References (102)

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Show Reference (102 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

1227

3553122

A single assay for simultaneously testing effectors of alanine racemase and/or D-alanine:D-alanine ligase

1987

Vicario, P.P.; Green, B.G.; Katzen, H.M.

J. Antibiot.

15

209-216

1230

-

Inhibition of D-alanyl-D-alanine ligase in different bacterial species by amino phosphonic acids

1979

Lacoste, A.M.; Poulsen, M.; Cassaigne, A.; Neuzil, E.

Curr. Microbiol.

2

113-117

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

1234

4567224

Biosynthesis of D-alanyl-D-alanine from L-alanine by extracts of a stabilized L-form fro Streptococcus pyogenes

1972

Pandhi, P.N.; Panos, C.

J. Gen. Microbiol.

71

487-494

1235

4552992

Studies on Escherichia coli enzymes involved in the synthesis of uridine diphosphate-N-acetyl-muramyl-pentapeptide

1972

Lugtenberg, E.J.J.

J. Bacteriol.

110

26-34

1236

1993184

Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes

1991

Zawadzke, L.E.; Bugg, T.D.H.; Walsh, C.T.

Biochemistry

30

1673-1682

2041

-

Amino acid racemase (Pseudomonas striata)

1971

Soda, K.; Osumi, T.

Methods Enzymol.

17

629-636

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

2088

-

Properties of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

1983

Ahmed, S.A.; Esaki, N.; Tanaka, H.; Soda, K.

Agric. Biol. Chem.

47

1887-1893

4750

5140194

alpha-Dialkyl acid transaminase from Pseudomonas cepacia. Purification, crystallization, physical, and kinetic properties

1971

Lamatiniere, C.A.; Itho, H.; Dempsey, W.B.

Biochemistry

10

4783-4788

6046

3275662

Diaminopropionate ammonia-lyase from Salmonella typhimurium. Purification and characterization of the crystalline enzyme and sequence determination of the pyridoxal 5'-phosphate binding peptide

1988

Nagasawa, T.; Tanizawa, K.; Satoda, T.; Yamada, H.

J. Biol. Chem.

263

958-964

32503

2269298

A novel nitrilase, arylacetonitrilase, of Alcaligenes faecalis JM3. Purification and characterization

1990

Nagasawa, T.; Mauger, J.; Yamada, H.

Eur. J. Biochem.

194

765-772

289263

4730493

Properties of crystalline Kynureninase from Pseudomonas marginalis

1973

Moriguchi, M.; Yamamoto, T.; Soda, K.

Biochemistry

12

2969-2974

289270

457635

Purification and properties of pig liver kynureninase

1979

Tanizawa, K.; Soda, K.

J. Biochem.

85

901-906

441393

-

Purification, physicochemical and regulatory properties of serine hydroxymethyltransferase from sheep liver

1982

Manohar, R.; Ramesh, K.S.; Rao, N.A.

J. Biosci.

4

31-50

441403

6821365

Purification and physicochemical, kinetic and immunological properties of allosteric serine hydroxymethyltransferase from monkey liver

1980

Ramesh, K.S.; Rao, N.A.

Biochem. J.

187

623-636

441408

16662139

Purification and regulatory properties of mung bean (Vigna Radiata L.) serine hydroxymethyltransferase

1982

Rao, D.N.; Rao, N.A.

Plant Physiol.

69

11-18

441410

3830156

Purification and characterization of a serine hydroxymethyltransferase from an obligate methylotroph, Hyphomicrobium methylovorum GM2

1987

Miyazaki, S.S.; Toki, S.; Izumi, Y.; Yamada, H.

Eur. J. Biochem.

162

533-540

441411

-

Futher characterization of serine hydroxymethyltransferase from a serine-producing methylotroph, Hyphomicrobium methylovorum

1987

Miyazaki, S.S.; Toki, S.; Izumi, Y.; Yamada, H.

Agric. Biol. Chem.

51

2587-2589

441416

6487593

Kinetic mechanism of the interaction of D-cycloserine with serine hydroxymethyltransferase

1984

Manohar, R.; Rao, A.G.A.; Rao, N.A.

Biochemistry

23

4116-4122

441420

7036682

Serine hydroxymethyltransferase

1982

Schirch, L.

Adv. Enzymol. Relat. Areas Mol. Biol.

53

83-112

441427

10762066

Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase - a potential target for cancer chemotherapy

2000

Appaji Rao, N.; Talwar, R.; Savithri, H.S.

Int. J. Biochem. Cell Biol.

32

405-416

485776

-

alpha-Methylserine transhydroxymethylase (Pseudomonas)

1971

Wilson Miles, E.

Methods Enzymol.

17B

341-346

485777

14001018

Metabolism of alpha-methylserine. I. Alpha-methylserine hydroxymethyltransferase

1962

Wilson, E.M.; Snell, E.E.

J. Biol. Chem.

237

3171-3179

487052

-

Partial purification and some properties of a 7-keto-8-aminopelargonic acid synthetase, an enzyme involved in biotin biosynthesis

1973

Izumi, Y.; Morita, H.; Tani, Y.; Ogata, K.

Agric. Biol. Chem.

37

1327-1333

492260

2804141

Purification and properties of isopenicillin-N epimerase from Streptomyces clavuligerus

1989

Usui, S.; Yu, C.A.

Biochim. Biophys. Acta

999

78-85

636678

3003495

Taurine-glutamate transaminase

1985

Yonaha, K.; Toyama, S.; Soda, K.

Methods Enzymol.

113

102-108

636679

629994

Properties of taurine: alpha-ketoglutarate aminotransferase of Achromobacter superficialis. Inactivation and reactivation of enzyme

1978

Toyama, S.; Misono, H.; Soda, K.

Biochim. Biophys. Acta

523

75-81

636706

6406228

Purification and properties of 2-aminoethylphosphonate:pyruvate aminotransferase from Pseudomonas aeruginosa

1983

Dumora, C.; Lacoste, A.M.; Cassaigne, A.

Eur. J. Biochem.

133

119-125

636737

5835935

D-Alanine-D-glutamate transaminase. II. Inhibitors and the mechanism of transamination of D-amino acids

1965

Martinez-Carrion, M.; Jenkins, W.T.

J. Biol. Chem.

240

3547-3552

636738

4710577

Occurrence of D-amino acid aminotransferase in pea seedlings

1973

Ogawa, T.; Fukuda, M.

Biochem. Biophys. Res. Commun.

52

998-1002

636742

1158891

D-amino acid aminotransferase of Bacillus sphaericus. Enzymologic and spectrometric properties

1975

Yonaha, K.; Misono, H.; Yamamoto, T.; Soda, K.

J. Biol. Chem.

250

6983-6989

637043

6688075

Inhibitory effect of 6-azauracil on purified rabbit liver 4-aminobutyrate aminotransferase

1983

Tamaki, N.; Kubo, K.; Aoyama, H.; Funatsuka, A.

J. Biochem.

93

955-959

637056

7362249

gamma-Aminobutyrate:alpha-ketoglutarate aminotransferase from Pseudomonas sp. F-126: purification, crystallization, and enzymologic properties

1980

Yonaha, K.; Toyama, S.

Arch. Biochem. Biophys.

200

156-164

637059

3917915

4-Aminobutyrate:2-oxoglutarate aminotransferase of Streptomyces griseus: purification and properties

1985

Yonaha, K.; Suzuki, K.; Toyama, S.

Eur. J. Biochem.

146

101-106

637090

-

Biosynthesis of biotin by microorganisms. XV. 7,8-Diaminopelargonic acid aminotransferase, an enzyme involved in biotin biosynthesis by microorganisms

1975

Izumi, Y.; Sato, K.; Tani, Y.; Ogata, K.

Agric. Biol. Chem.

39

175-181

637254

3099645

Kinetic properties and characteristics of mouse liver mitochondrial asparagine aminotransferase

1986

Maul, D.M.; Schuster, S.M.

Arch. Biochem. Biophys.

251

585-593

637347

6373737

Enzymatic proof for the identity of the S-sulfocysteine synthase and cysteine synthase B of Salmonella typhimurium

1984

Nakamura, T.; Iwahashi, A.; Eguchi, Y.

J. Bacteriol.

158

1122-1127

637347

6373737

Enzymatic proof for the identity of the S-sulfocysteine synthase and cysteine synthase B of Salmonella typhimurium

1984

Nakamura, T.; Iwahashi, H.; Eguchi, Y.

J. Bacteriol.

158

1122-1127

637347

2 entries

637439

3816790

Purification and characterization of cystathionine gamma-synthase type II from Bacillus sphaericus

1987

Kanzaki, H.; Kobayashi, M.; Nagasawa, T.; Yamada, H.

Eur. J. Biochem.

163

105-112

644426

2158891

Purification, characterization and inhibition of D-3-aminoisobutyrate aminotransferase from the rat liver

1990

Tamaki, N.; Kaneko, M.; Mizota, C.; Kikugawa, M.; Fujimoto, S.

Eur. J. Biochem.

189

39-45

649337

12499203

Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine

2003

Feng, Z.; Barletta, R.G.

Antimicrob. Agents Chemother.

47

283-291

650876

11026672

Purification and properties of alanine racemase from crayfish Procambarus clarkii

2000

Shibata, K.; Shirasuna, K.; Motegi, K.; Kera, Y.; Abe, H.; Yamada, R.

Comp. Biochem. Physiol. B

126

599-608

650892

12568809

Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii

2003

Shibata, K.; Watanabe, T.; Yoshikawa, H.; Abe, K.; Takahashi, S.; Kera, Y.; Yamada, R.H.

Comp. Biochem. Physiol. B

134

307-314

652809

10556038

Crystal structures of dialkylglycine decarboxylase inhibitor complexes

1999

Malashkevich, V.N.; Strop, P.; Keller, J.W.; Jansonius, J.N.; Toney, M.D.

J. Mol. Biol.

294

193-200

652963

10937441

Modeling of Enterococcus faecalis D-alanine:D-alanine ligase: structure-based study of the active site in the wild-type enzyme and in glycopeptide-dependent mutants

2000

Prevost, M.; Van Belle, D.; Tulkens, P.M.; Courvalin, P.; Van Bambeke, F.

J. Mol. Microbiol. Biotechnol.

2

321-330

661196

15807525

Effect of a Y265F mutant on the transamination-based cycloserine inactivation of alanine racemase

2005

Fenn, T.D.; Holyoak, T.; Stamper, G.F.; Ringe, D.

Biochemistry

44

5317-5327

662288

15302885

Self-protection mechanism in D-cycloserine-producing Streptomyces lavendulae. Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase, which are target enzymes of D-cycloserine

2004

Noda, M.; Kawahara, Y.; Ichikawa, A.; Matoba, Y.; Matsuo, H.; Lee, D.G.; Kumagai, T.; Sugiyama, M.

J. Biol. Chem.

279

46143-46152

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