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Information on EC 6.3.2.4 - D-Alanine-D-alanine ligase and Organism(s) Thermus thermophilus and UniProt Accession Q5SHZ3
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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
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d-alanyl-d-lactate
- teicoplanin
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depsipeptide
- d-ala-d-lac
- drug development
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vanrs
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atp-grasp
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vancomycin-dependent
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vand-type
- d-ala-d-lactate
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d-ala2
- analysis
- synthesis
The taxonomic range for the selected organisms is: Thermus thermophilus
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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D-Ala-D-Ala synthetase
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D-Alanine:D-alanine ligase
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D-Alanyl-D-alanine synthetase
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D-Alanylalanine synthetase
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Synthetase, D-alanylalanine
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VanA
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VanB ligase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylic acid amide formation
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carboxamide formation
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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
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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-Ala + NH3
ADP + phosphate + D-AlaNH2
the D-AlaNH2 production of enzyme S293X mutants is optimized, the S293E variant, which is selected as the best enzyme for D-AlaNH2 production, exhibits an optimal activity at pH 9.0 and 40°C for D-AlaNH2 production. The S293E variant catalyzes the synthesis of 9.3 and 35.7 mM of D-AlaNH2 from 10 and 50 mM D-Ala and 3 M NH4Cl with conversion yields of 93% and 71.4%, respectively. The S293E variant exhibits higher reaction specificity to D-AlaNH2 production compared with the S293D variant and the other variants
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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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten steady-state kinetics
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additional information
additional information
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Michaelis-Menten steady-state kinetics
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
homology structure modeling analyses of wild-type enzyme and mutants S293D and S293E. Both amino acids Arg268 and Ser293 play an important role in the synthesis of D-Ala-D-Ala, residue Ser293 recognizes the carboxylate group of D-Ala2, but is not involved in the ATP hydrolysis, while the Arg268 residue recognizes the carboxylate group of D-Ala1 and is involved in ATP hydrolysis to form the activated acyl-phosphate intermediate. Ligand docking simulations
additional information
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homology structure modeling analyses of wild-type enzyme and mutants S293D and S293E. Both amino acids Arg268 and Ser293 play an important role in the synthesis of D-Ala-D-Ala, residue Ser293 recognizes the carboxylate group of D-Ala2, but is not involved in the ATP hydrolysis, while the Arg268 residue recognizes the carboxylate group of D-Ala1 and is involved in ATP hydrolysis to form the activated acyl-phosphate intermediate. Ligand docking simulations
PDB
SCOP
CATH
UNIPROT
ORGANISM
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S293A
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293C
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293D
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with high production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293E
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with high production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293F
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293G
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293H
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293I
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with high production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293K
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293L
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293M
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with high production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293N
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293P
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme, it catalyzes the synthesis of both D-AlaNH2 and D-Ala-dDAla
S293Q
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293R
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme, it catalyzes the synthesis of both D-AlaNH2 and D-Ala-D-Ala
S293S
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293T
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293V
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with high production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293W
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
S293Y
site-directed mutagenesis, the mutant shows altered substrate specificity compared to wild-type enzyme with production of D-AlaNH2 from D-Ala and NH3 in contrast to the wild-type enzyme
additional information
additional information
homology structure modeling analyses of wild-type enzyme and mutants S293D and S293E
additional information
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homology structure modeling analyses of wild-type enzyme and mutants S293D and S293E
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity and anion exchange chromatography, followed by dialysis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene dll, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Miki, Y.; Okazaki, S.; Asano, Y.
Engineering an ATP-dependent D-Ala D-Ala ligase for synthesizing amino acid amides from amino acids
J. Ind. Microbiol. Biotechnol.
44
667-675
2017
Thermus thermophilus (Q5SHZ3), Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q5SHZ3)
EXTERNAL LINKS (specific for EC-Number 6.3.2.4)
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Release 2023.1 (January 2023)
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