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Information on EC 6.3.2.4 - D-Alanine-D-alanine ligase and Organism(s) Helicobacter pylori and UniProt Accession Q2N4T5
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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
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atp-grasp
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vancomycin-dependent
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vand-type
- d-ala-d-lactate
-
d-ala2
- analysis
- synthesis
The taxonomic range for the selected organisms is: Helicobacter pylori
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-alanyl-d-alanine synthetase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D-Ala-D-Ala ligase
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-
-
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D-Ala-D-Ala synthetase
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-
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D-Alanine:D-alanine ligase
D-Alanyl-D-alanine synthetase
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-
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D-Alanylalanine synthetase
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-
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Synthetase, D-alanylalanine
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-
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VanA
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-
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VanB ligase
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-
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additional information
the enzyme is a member of the D-Ala-D-X ligase superfamily
D-Alanine:D-alanine ligase
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylic acid amide formation
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-
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carboxamide formation
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-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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-, -, -
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 + D-alanine
ADP + phosphate + D-alanyl-D-alanine
the enzyme shows relatively weak binding affinity and poor catalytic activity against the substrate D-Ala in vitro, active site structure, overview
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-
?
additional information
?
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no activity with D-Ser, Gly, and D-lactate
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-
?
additional information
?
-
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no activity with D-Ser, Gly, and D-lactate
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-
?
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
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
apigenin
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4',5,7-trihydroxyflavone, inhibition mechanism, competitive with respect to the substrate ATP and non-competitive to the substrate D-Ala
quercetin
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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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
kinetics of wild-type and mutant enzymes
-
additional information
additional information
-
kinetics of wild-type and mutant enzymes
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
3_10-helix, including residues from Gly306 to Leu312, near the D-Ala binding region in the C-terminal domain probably participates in D-Ala binding and conformational change of the enzyme
additional information
-
3_10-helix, including residues from Gly306 to Leu312, near the D-Ala binding region in the C-terminal domain probably participates in D-Ala binding and conformational change of the enzyme
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme, 4-8 mg/ml protien in 20 mM Tris-HCl, pH 8.0, 300 mM NaCl, 2 mM MgCl2, hanging drop vapour diffusion method, 4°C, versus a reservoir solution containing 0.1M HEPES, pH 7.5, 10% PEG 6000, 5% MPD, 4 months, X-ray diffraction structure determination and analysisat 2.4 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
I16V
site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure
L241F
site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure
L241Y
site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure
L308T
site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure
Y311S
site-directed mutagenesis of an active site mutant, mutant kinetics compared to the wild-type structure
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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