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Information on EC 6.3.2.4 - D-Alanine-D-alanine ligase and Organism(s) Escherichia coli and UniProt Accession P07862
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6.3.2.4 D-Alanine-D-alanine ligaseIUBMB Comments
Involved with EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---L-lysine ligase) or EC 6.3.2.13 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate---L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoyl-L-alanine---D-glutamate ligase) and EC 6.3.2.10 (UDP-N-acetylmuramoyl-tripeptide---D-alanyl-D-alanine ligase) in the synthesis of a cell-wall peptide (click here for diagram).
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Word Map
- 6.3.2.4
- peptidoglycan
- vancomycin
-
enterococci
- d-cycloserine
-
vancomycin-resistant
- faecium
-
d-alanyl-d-lactate
- teicoplanin
-
depsipeptide
- d-ala-d-lac
- drug development
-
vanrs
-
atp-grasp
-
vancomycin-dependent
-
vand-type
- d-ala-d-lactate
-
d-ala2
- analysis
- synthesis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
d-alanine:d-alanine ligase, d-alanine-d-alanine ligase, d-ala-d-ala ligase, d-ala:d-ala ligase, vanb ligase, ttddl, abddl, tmddl, ecddlb, d-alanine:d-alanine (d-lactate) ligase (adp), 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D-Ala-D-Ala ligase
-
-
-
-
D-Ala-D-Ala synthetase
-
-
-
-
D-Alanine:D-alanine ligase
D-Alanyl-D-alanine synthetase
-
-
-
-
D-Alanylalanine synthetase
-
-
-
-
Synthetase, D-alanylalanine
-
-
-
-
VanA
-
-
-
-
VanB ligase
-
-
-
-
D-Alanine:D-alanine ligase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
reaction mechanism via tetrahedral reaction intermediate, overview
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylic acid amide formation
-
-
-
-
carboxamide formation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
D-alanine:D-alanine ligase (ADP-forming)
Involved with EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---L-lysine ligase) or EC 6.3.2.13 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---2,6-diaminopimelate ligase), EC 6.3.2.8 (UDP-N-acetylmuramate---L-alanine ligase), EC 6.3.2.9 (UDP-N-acetylmuramoyl-L-alanine---D-glutamate ligase) and EC 6.3.2.10 (UDP-N-acetylmuramoyl-tripeptide---D-alanyl-D-alanine ligase) in the synthesis of a cell-wall peptide (click here for diagram).
CAS REGISTRY NUMBER
COMMENTARY
9023-63-6
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + Ala + Ala
?
-
a possible cellular role of VanA is to synthesize a modified cell-wall component, with D-Ala-D-Met or D-Ala-Phe instead of D-Ala-D-Ala, which is subsequently not recognized by vancomycin
-
-
?
ATP + D-Ala + 2-aminopentanoate
ADP + phosphate + D-Ala-2-aminopentanoate
-
-
-
-
?
ATP + D-Ala + D-2-aminopentanoate
ADP + phosphate + D-Ala-D-2-aminopentanoate
-
-
-
-
?
ATP + D-Ala + D-norleucine
ADP + phosphate + D-Ala-D-norleucine
-
-
-
-
?
ATP + D-alanine + D-serine
ADP + D-alanyl-D-serine + D-alanyl-D-alanine + D-seryl-D-serine
-
-
-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
Y216, S150, and E15 form a hydrogen-bonding triad that orients an omega-loop to close over the active site and also to orient substrate D-Ala1 (the first molecule of substrate that is activated by the enzyme protein). The bifunctional enzyme also catalyzes the formation of D-alanyl-D-lactate (D-alanine-(R)-lactate ligase)
-
-
?
additional information
?
-
DDl is an essential enzyme in bacterial cell wall biosynthesis
-
-
?
additional information
?
-
-
the enzyme is also capable of synthesizing fluorinated dipeptides
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + Ala + Ala
?
-
a possible cellular role of VanA is to synthesize a modified cell-wall component, with D-Ala-D-Met or D-Ala-Phe instead of D-Ala-D-Ala, which is subsequently not recognized by vancomycin
-
-
?
additional information
?
-
DDl is an essential enzyme in bacterial cell wall biosynthesis
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(E)-N-(2-chloroethyl)-N'-(4-isopropylphenyl)diazene-1,2-dicarboxamide
-
(E)-N-(2-chloroethyl)-N'-(pyridin-2-ylmethyl)diazene-1,2-dicarboxamide
-
(E)-N-(2-chloroethyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
-
(E)-N-(3-chlorophenyl)-N'-(pyridin-3-ylmethyl)diazene-1,2-dicarboxamide
-
(E)-N-(3-chlorophenyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
-
(E)-N-(4-fluorophenyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
-
(E)-N-(4-sec-butylphenyl)-N'-(2-chloroethyl)diazene-1,2-dicarboxamide
-
(E)-N-[4-(butan-2-yl)phenyl]-N'-(2-chloroethyl)diazene-1,2-dicarboxamide
-
LFM-A13
Brutons's tyrosine kinase inhibitor, an analog of the Leflunomide metabolite A771726
phospho-D-cycloserine
DCSP, inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine, DCS, bimodal mechanism of action of the inhibitor. The compound also inhibits the phosphatase activity of EcDdlB, formation of phospho-D-cycloserine by EcDdlB in solution a positional isotope exchange (PIX) reaction, a phosphatase activity of EcDdlB is detected as a side-reaction alongside the positional isotope exchange (PIX) reaction. DCS is the specific acceptor of the ATP gamma-P group during the phosphate transfer reaction by the enzyme, and DCS inhibits EcDdlB phosphatase activity
1-(3-chloro-8-methoxy-11H-indolo[3,2-c]quinolin-9-yl)-N,N-dimethylmethanamine
-
-
1-tert-butyl-3-[6-(2,6-dichlorophenyl)-2-[[3-(morpholin-4-yl)propyl]amino]pyrido[2,3-d]pyrimidin-7-yl]urea
-
-
1-tert-butyl-3-[6-(3,5-dimethoxyphenyl)-2-[[3-(dimethylamino)propyl]amino]pyrido[2,3-d]pyrimidin-7-yl]urea
-
-
1-tert-butyl-3-[6-(3,5-dimethoxyphenyl)-2-[[3-(morpholin-4-yl)propyl]amino]pyrido[2,3-d]pyrimidin-7-yl]urea
-
-
1-[2-amino-6-(1,3-benzodioxol-5-yl)pyrido[2,3-d]pyrimidin-7-yl]-3-tert-butylurea
-
-
1-[2-amino-6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidin-7-yl]-3-tert-butylurea
-
-
1-[2-amino-6-(2-bromo-6-fluorophenyl)pyrido[2,3-d]pyrimidin-7-yl]-3-tert-butylurea
-
-
1-[2-amino-6-(3,5-dimethoxyphenyl)pyrido[2,3-d]pyrimidin-7-yl]-3-tert-butylurea
-
-
1-[2-amino-6-[3,5-bis(trifluoromethyl)phenyl]pyrido[2,3-d]pyrimidin-7-yl]-3-tert-butylurea
-
-
1-[4-[(6-chloro-2-methoxyacridin-9-yl)amino]phenyl]-3-(dimethylamino)propan-1-ol
-
-
1-[[(4-fluorophenyl)sulfonyl]amino]-3-(morpholin-4-yl)propan-2-yl dihydrogen phosphate
-
0.5 mM, 77% inhibition
1-[[(4-methoxyphenyl)sulfonyl]amino]-3-(morpholin-4-yl)propan-2-yl dihydrogen phosphate
-
0.5 mM, 83% inhibition
2,2-diethoxy-N-[(6-methoxy-1,4-dimethyl-9H-carbazol-3-yl)methyl]ethanamine
-
-
2,2-diethoxy-N-[(7-fluoro-1,4-dimethyl-9H-carbazol-3-yl)methyl]ethanamine
-
-
2,2-diethoxy-N-[(8-ethyl-1,4-dimethyl-9H-carbazol-3-yl)methyl]ethanamine
-
-
2-[(1-[[2-amino-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-7-yl]amino]ethenyl)amino]propan-2-ol
-
-
2-[(1-[[2-amino-6-(2,6-difluorophenyl)pyrido[2,3-d]pyrimidin-7-yl]amino]ethenyl)amino]propan-2-ol
-
-
2-[(1-[[2-amino-6-(3,5-dichlorophenyl)pyrido[2,3-d]pyrimidin-7-yl]amino]ethenyl)amino]propan-2-ol
-
-
2-[(1-[[2-amino-6-(3,5-difluorophenyl)pyrido[2,3-d]pyrimidin-7-yl]amino]ethenyl)amino]propan-2-ol
-
-
3-[(1,6-dichloro-4-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]phenol
-
-
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-(pyrrolidin-1-ylmethyl)phenol
-
-
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(4-methylpiperazin-1-yl)methyl]phenol
-
-
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]-6-(prop-2-en-1-yl)phenol
-
-
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]phenol
-
-
6-(2,6-dichlorophenyl)-N2-[3-(dimethylamino)propyl]pyrido[2,3-d]pyrimidine-2,7-diamine
-
-
6-(2,6-dichlorophenyl)-N2-[3-(morpholin-4-yl)propyl]pyrido[2,3-d]pyrimidine-2,7-diamine
-
-
6-(3,5-dimethoxyphenyl)-N2-[3-(morpholin-4-yl)propyl]pyrido[2,3-d]pyrimidine-2,7-diamine
-
-
apigenin
-
4',5,7-trihydroxyflavone, inhibition mechanism, competitive with respect to the substrate ATP and non-competitive to the substrate D-Ala
N-[(3-chloro-8-methoxy-11H-indolo[3,2-c]quinolin-9-yl)methyl]-N-ethylethanamine
-
-
N-[(6-bromo-1,4-dimethyl-9H-carbazol-3-yl)methyl]-2,2-diethoxyethanamine
-
-
Phosphonate dipeptide analogs
-
weak inhibition of ligase B from E. coli and Van A from Enterococcus faecium
-
quercetin
-
i.e. 3,3',4',5,7-pentahydroxyflavone, inhibition mechanism, competitive with respect to the substrate ATP and non-competitive to the substrate D-Ala
[1(S)-Aminoethyl][(2RS)2-carboxy-1-octyl]phosphinic acid
-
classical slow-binding
Phosphinates
-
weak inhibition of ligase B of E. coli and Van A from Enterococcus faecium, strong inhibition of ligase A from E. coli
-
additional information
antibiotic inhibitor design, bisubstrate inhibitors that block the ATP and D-Ala binding sites exhibit enhanced selectivity and potency profiles by preferentially inhibiting DDl over kinases, overview
-
additional information
-
6-arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of the bacterial enzyme, ligand docking and modeling, overview
-
additional information
-
evaluation of ellipticines and 9-acridinylamines as enzyme inhibitors. Ellipticines with a quaternary methylpyridinium moiety are the most potent among all studied compounds, with MIC values as low as 2 mg/l in strains with intact efflux mechanisms. The compounds cause membrane damage. Inhibitor MIC values, overview
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.003
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule) , wild-type enzyme, pH 7.5
0.004
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), wild-type enzyme, pH 9.2
0.11
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), wild-type enzyme, pH 6.0
0.51
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 7.5
0.51
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 9.2
0.85
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme S150A, pH 7.5
1.1
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), wild-type enzyme, pH 9.2
2
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), wild-type enzyme, pH 7.5
4.8
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme Y216F, pH 9.2
6.2
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme S150A, pH 6.0
8
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), wild-type enzyme, pH 6.0
11
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 6.0
16
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule), mutant enzyme Y216F, pH 7.5
44
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule) , mutant enzyme S150A, pH 9.2
65
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 9.2
74
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 7.5
80
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme S150A, pH 7.5
82
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme E15Q, pH 6.0
140
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme S150A, pH 6.0
150
D-alanine
37°C, KM-value for D-alanine1 (the first molecule of substrate that is activated by the enzyme molecule) , mutant enzyme Y216F, pH 6.0
450
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme Y216F, pH 6.0
630
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme Y216F, pH 7.5
1100
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme S150A, pH 9.2
1200
D-alanine
37°C, KM-value for D-alanine2 (the second molecule of substrate that is activated by the enzyme molecule), mutant enzyme Y216F, pH 9.2
additional information
additional information
steady-state kinetics of ATP hydrolysis
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
turnover numbers of wild-type and mutant enzyme forms
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.4
D-alanine
37°C, mutant enzyme S150A, kcat/Km(D-alanine2), pH 6.0. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
2.4
D-alanine
37°C, mutant enzyme E15Q, kcat/Km(D-alanine2), pH 6.0. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
3
D-alanine
37°C, mutant enzyme Y216F, kcat/Km(D-alanine2), pH 6.0. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
11
D-alanine
37°C, mutant enzyme E15Q, kcat/Km(D-alanine2), pH 7.5. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
12
D-alanine
37°C, mutant enzyme S150A, kcat/Km(D-alanine2), pH 7.5. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
17
D-alanine
37°C, mutant enzyme E15Q, kcat/Km(D-alanine2), pH 9.2. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
26
D-alanine
37°C, mutant enzyme S150A, kcat/Km(D-alanine2), pH 9.2. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
39
D-alanine
37°C, mutant enzyme Y216F, kcat/Km(D-alanine2), pH 7.5. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
89
D-alanine
37°C, wild-type enzyme, kcat/Km(D-alanine2), pH 6.0. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
260
D-alanine
37°C, mutant enzyme Y216F, kcat/Km(D-alanine2), pH 9.2. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
440
D-alanine
37°C, wild-type enzyme, kcat/Km(D-alanine2), pH 7.5. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
1500
D-alanine
37°C, wild-type enzyme, kcat/Km(D-alanine2), pH 9.2. D-Alanine2 is the second molecule of substrate that is activated by the enzyme molecule
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
inhibition kinetics at pH 7.4 and 25°C
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.049
(E)-N-(2-chloroethyl)-N'-(4-isopropylphenyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.119
(E)-N-(2-chloroethyl)-N'-(pyridin-2-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.236
(E)-N-(2-chloroethyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.073
(E)-N-(4-fluorophenyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.025
(E)-N-(4-sec-butylphenyl)-N'-(2-chloroethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.121
(E)-N-cyclohexyl-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.111
(E)-N-phenyl-N'-(pyridin-2-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.106
(E)-N-phenyl-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.025
(E)-N-[4-(butan-2-yl)phenyl]-N'-(2-chloroethyl)diazene-1,2-dicarboxamide
Escherichia coli
pH 8.0, 37°C
0.135
1-[4-[(6-chloro-2-methoxyacridin-9-yl)amino]phenyl]-3-(dimethylamino)propan-1-ol
Escherichia coli
-
pH 8.0, 37°C
0.07
3-(9-methoxy-5,11-dimethyl-6H-pyrido[4,3-b]carbazol-6-yl)propan-1-amine
Escherichia coli
-
pH 8.0, 37°C
0.119
3-[(1,6-dichloro-4-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]phenol
Escherichia coli
-
pH 8.0, 37°C
0.102
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-(pyrrolidin-1-ylmethyl)phenol
Escherichia coli
-
pH 8.0, 37°C
0.162
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(4-methylpiperazin-1-yl)methyl]phenol
Escherichia coli
-
pH 8.0, 37°C
0.161
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]-6-(prop-2-en-1-yl)phenol
Escherichia coli
-
pH 8.0, 37°C
0.32
3-[(6-chloro-2-methoxyacridin-9-yl)amino]-2-[(diethylamino)methyl]phenol
Escherichia coli
-
pH 8.0, 37°C
0.064
8-fluoro-2,5,11-trimethyl-6H-pyrido[4,3-b]carbazol-2-ium iodide
Escherichia coli
-
pH 8.0, 37°C
0.023
9-bromo-2,5,11-trimethyl-6H-pyrido[4,3-b]carbazol-2-ium iodide
Escherichia coli
-
pH 8.0, 37°C
0.036
9-bromo-2,5,6,11-tetramethyl-6H-pyrido[4,3-b]carbazol-2-ium iodide
Escherichia coli
-
pH 8.0, 37°C
0.089
9-methoxy-2,5,11-trimethyl-6H-pyrido[4,3-b]carbazol-2-ium acetate
Escherichia coli
-
pH 8.0, 37°C
0.065
9-methoxy-2,5,11-trimethyl-6H-pyrido[4,3-b]carbazol-2-ium iodide
Escherichia coli
-
pH 8.0, 37°C
0.043
9-methoxy-2,5,6,11-tetramethyl-6H-pyrido[4,3-b]carbazol-2-ium iodide
Escherichia coli
-
pH 8.0, 37°C
0.33 - 0.623
N-[(3-chloro-8-methoxy-11H-indolo[3,2-c]quinolin-9-yl)methyl]-N-ethylethanamine
0.015
(E)-N-(3-chlorophenyl)-N'-(pyridin-3-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.015
(E)-N-(3-chlorophenyl)-N'-(pyridin-3-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
pH 8.0, 37°C
0.033
(E)-N-(3-chlorophenyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.033
(E)-N-(3-chlorophenyl)-N'-(pyridin-4-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
pH 8.0, 37°C
0.036
(E)-N-phenyl-N'-(pyridin-3-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
-
0.036
(E)-N-phenyl-N'-(pyridin-3-ylmethyl)diazene-1,2-dicarboxamide
Escherichia coli
pH 8.0, 37°C
0.032
6-chloro-2-methoxy-N-(6-methoxyquinolin-8-yl)acridin-9-amine
Escherichia coli
-
pH 8.0, 37°C
0.09
6-chloro-2-methoxy-N-(6-methoxyquinolin-8-yl)acridin-9-amine
Escherichia coli
-
pH 8.0, 37°C
0.33
N-[(3-chloro-8-methoxy-11H-indolo[3,2-c]quinolin-9-yl)methyl]-N-ethylethanamine
Escherichia coli
-
pH 8.0, 37°C
0.623
N-[(3-chloro-8-methoxy-11H-indolo[3,2-c]quinolin-9-yl)methyl]-N-ethylethanamine
Escherichia coli
-
pH 8.0, 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
-
D-alanine:D-alanine ligase is an intracellular bacterial enzyme essential for cell wall biosynthesis
physiological function
-
the enzyme catalyzes the formation of the terminal D-Ala-D-Ala dipeptide of the peptidoglycan precursor UDP-MurNAc pentapeptide
PDB
SCOP
CATH
UNIPROT
ORGANISM
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
complexed with a D-Ala-D-2-hydroxybutanoate phosphonate, and Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate, at 2.2A and 1.9A resolution
purified recombinant His-tagged enzyme in complex with ATP and D-alanyl-D-alanine, or with ATD and D-alanyl-D-alanine, or with inhibitor D-cycloserine and ADP, hanging drop method, mixing of 0.002 ml of 12 mg/ml protein in 50 mM HEPES, pH 7.5, 150 mM KCl, 0.5 mM EDTA, 5 mM ATP or 5 mM ADP, and 50 mM D-alanyl-D-alanine, with 0.002 ml of reservoir solution containing 200 mM MgCl2, 25% PEG 3350, 100 mM TrisHCl pH 8.0, 18°C, X-ray diffraction structure determination and analysis at 1.4-1.65 A resolution, active site region of EcDdlB in the different complexes, overview
co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, at 2.3 A resolution
-
in ternary complex with ADP and D-alanyl-D-alanine, to 1.4 A resolution, and with the ligands ATP and D-alanyl-D-alanine, representing the product-inhibited complex, to 1.5 A resolution
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E15Q
mutant enzyme with negligible depsipeptide synthetase activity. The mutant uniquely activates D-Lac as the electrophilic rather than the nucleophilic partner for condensation with D-Ala to make a regioisomeric D-Lac-D-Ala, an amide rather than an ester product
S150A
mutant has gained depsipeptide (D-Ala-D-Lac, D-Ala-D-hydroxybutyrate) ligase activity with dipeptide/depsipeptide partition ratios that mimic the pH behavior of VanA (D-alanine(R)-lactate ligase)
Y216F
mutant has gained depsipeptide (D-Ala-D-Lac, D-Ala-D-hydroxybutyrate) ligase activity with dipeptide/depsipeptide partition ratios that mimic the pH behavior of VanA (D-alanine(R)-lactate ligase)
L282R
-
11fold decrease in kcat for D-alanine, 18fold increase in Km for D-alanine, 23fold decrease in Km for D-serine, 9fold drop in kcat for D-serine
additional information
-
mutant enzymes at K144, K215, and E270 in the ATP binding site, at E15, S150, H63, and R255 in the first D-Ala subsite, and at Y216, S281, L282, and D257 in the second D-Ala subsite. Mutant enzymes E270Q, K215A, R255A, and D257N retain very low or no detectable activity. Mutants enzyme Y216F shows substantial retention of activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His-tagged enzyme from Escherichia coli strain BL21(lambdaDE3)StarpRosetta by nickel affinity chromatography and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene ddlB, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(lambdaDE3)StarpRosetta
expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain JM109
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
the enzyme is a target for antibiotic inhibitor development, overview
drug development
drug development
-
the enzyme is an attractive and viable target in the search for effective antimicrobial drugs
drug development
-
the enzyme is an attractive target for development of antimicrobial drugs
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shi, Y.; Walsh, C.T.
Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis
Biochemistry
34
2768-2776
1995
Escherichia coli
Lugtenberg, E.J.J.; van Schijndel-van Dam, A.
Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase
J. Bacteriol.
113
96-104
1973
Escherichia coli
Bugg, T.D.H.; Dutka-Malen, S.; Athur, M.; Courvalin, P.; Walsh, C.T.
Identification of vancomycin resistance protein VanA as a D-alanine:D-alanine ligase of altered substrate specificity
Biochemistry
30
2017-2021
1991
Escherichia coli, Escherichia coli JM105
Lugtenberg, E.J.J.
Studies on Escherichia coli enzymes involved in the synthesis of uridine diphosphate-N-acetyl-muramyl-pentapeptide
J. Bacteriol.
110
26-34
1972
Escherichia coli
Zawadzke, L.E.; Bugg, T.D.H.; Walsh, C.T.
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
Biochemistry
30
1673-1682
1991
Escherichia coli
Fan, C.; Park, I.S.; Walsh, C.T.; Knox, J.R.
D-Alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant
Biochemistry
36
2531-2538
1997
Escherichia coli (P07862), Escherichia coli
Duncan, K.; van Heijenoort, J.; Walsh, C.T.
Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli
Biochemistry
29
2379-2386
1990
Escherichia coli
Ellsworth, B.A.; Tom, N.J.; Bartlett, P.A.
Synthesis and evaluation of inhibitors of bacterial D-alanine:D-alanine ligases
Chem. Biol.
3
37-44
1996
Escherichia coli, Enterococcus faecium
Al-Bar, O.A.M.; OConnor, C.D.; Giles, I.G.; Akhtar, M.
D-Alanine:D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme
Biochem. J.
282
747-752
1992
Escherichia coli
Fan, C.; Moews, P.C.; Walsh, C.T.; Knox, J.R.
Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution
Science
266
439-443
1994
Escherichia coli
Healy, V.L.; Park, I.S.; Walsh, C.T.
Active-site mutants of the VanC2 D-alanyl-D-serine ligase, characteristic of one vancomycin-resistant bacterial phenotype, revert towards wild-type D-alanyl-D-alanine ligases
Chem. Biol.
5
197-207
1998
Escherichia coli
Sato, M.; Kirimura, K.; Kino, K.
D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity
J. Biosci. Bioeng.
99
623-628
2005
Escherichia coli, Oceanobacillus iheyensis, Synechocystis sp. PCC 6803, Thermotoga maritima, Oceanobacillus iheyensis JCM 11309
Kovac, A.; Majce, V.; Lenarsic, R.; Bombek, S.; Bostock, J.M.; Chopra, I.; Polanc, S.; Gobec, S.
Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl)
Bioorg. Med. Chem. Lett.
17
2047-2054
2007
Escherichia coli (P07862), Escherichia coli
Triola, G.; Wetzel, S.; Ellinger, B.; Koch, M.; Huebel, K.; Rauh, D.; Waldmann, H.
ATP competitive inhibitors of D-alanine-D-alanine ligase based on protein kinase inhibitor scaffolds
Bioorg. Med. Chem.
17
1079-1087
2008
Escherichia coli (P07862)
Wu, D.; Kong, Y.; Han, C.; Chen, J.; Hu, L.; Jiang, H.; Shen, X.
D-Alanine:D-alanine ligase as a new target for the flavonoids quercetin and apigenin
Int. J. Antimicrob. Agents
32
421-426
2008
Escherichia coli, Helicobacter pylori
Batson, S.; Rea, D.; Fueloep, V.; Roper, D.I.
Crystallization and preliminary X-ray analysis of a D-alanyl-D-alanine ligase (EcDdlB) from Escherichia coli
Acta Crystallogr. Sect. F
66
405-408
2010
Escherichia coli
Sova, M.; Cadez, G.; Turk, S.; Majce, V.; Polanc, S.; Batson, S.; Lloyd, A.J.; Roper, D.I.; Fishwick, C.W.; Gobec, S.
Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB)
Bioorg. Med. Chem. Lett.
19
1376-1379
2009
Enterococcus faecium, Escherichia coli
Park, I.-S.; Lin, C.-H.; Walsh, C.T.
Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B
Biochemistry
35
10464-10471
1996
Escherichia coli (P07862), Escherichia coli
Vehar, B.; Hrast, M.; Kovac, A.; Konc, J.; Mariner, K.; Chopra, I.; O'Neill, A.; Janezic, D.; Gobec, S.
Ellipticines and 9-acridinylamines as inhibitors of D-alanine:D-alanine ligase
Bioorg. Med. Chem.
19
5137-5146
2011
Escherichia coli
Skedelj, V.; Arsovska, E.; Tomasic, T.; Kroflic, A.; Hodnik, V.; Hrast, M.; Bester-Rogac, M.; Anderluh, G.; Gobec, S.; Bostock, J.; Chopra, I.; O'Neill, A.J.; Randall, C.; Zega, A.
6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase
PLoS ONE
7
e39922
2012
Escherichia coli
Batson, S.; de Chiara, C.; Majce, V.; Lloyd, A.J.; Gobec, S.; Rea, D.; Fueloep, V.; Thoroughgood, C.W.; Simmons, K.J.; Dowson, C.G.; Fishwick, C.W.G.; de Carvalho, L.P.S.; Roper, D.I.
Inhibition of D-Ala D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine
Nat. Commun.
8
1939
2017
Escherichia coli (P07862)
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